@@ Line 12: / Line 12: @@
 | align="center" | [http://www.simulia.com/products/abaqus_fea.html abaqus]
 | align="center" | phys
-| align="center" | 6.14.1, 2020, 2021
+| align="center" | 2021
 | Documentation: [[Abaqus]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA. Homepage: http://www.simulia.com/products/abaqus_fea.html URL: http://www.simulia.com/products/abaqus_fea.html Keyword:phys<br /><br /><br /></div>
 |-
 | align="center" | [http://www.abinit.org/ abinit]
 | align="center" | chem
-| align="center" | 8.4.4, 8.10.2, 9.2.1, 9.2.2, 9.6.2, 10.0.3
+| align="center" | 9.2.2, 9.6.2, 10.0.3
 | Documentation: [[ABINIT]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. Homepage: http://www.abinit.org/ URL: http://www.abinit.org/ Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 32: / Line 32: @@
 | align="center" | [https://www.bcgsc.ca/platform/bioinfo/software/abyss abyss]
 | align="center" | bio
-| align="center" | 2.0.2, 2.2.5, 2.3.7
+| align="center" | 2.2.5, 2.3.7
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler Homepage: https://www.bcgsc.ca/platform/bioinfo/software/abyss URL: https://www.bcgsc.ca/platform/bioinfo/software/abyss Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 40: / Line 40: @@
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ACTC converts independent triangles into triangle strips or fans. Homepage: https://sourceforge.net/projects/actc URL: https://sourceforge.net/projects/actc<br /><br /><br /></div>
 |-
-| align="center" | [http://software.genetics.ucla.edu/admixture admixture]
+| align="center" | [https://dalexander.github.io/admixture/ admixture]
 | align="center" | bio
 | align="center" | 1.3.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. Homepage: http://software.genetics.ucla.edu/admixture URL: http://software.genetics.ucla.edu/admixture Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. Homepage: https://dalexander.github.io/admixture/ URL: https://dalexander.github.io/admixture/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://projects.coin-or.org/ADOL-C adol-c]
 | align="center" | -
-| align="center" | 2.6.3, 2.7.0, 2.7.2
+| align="center" | 2.7.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The package ADOL-C (Automatic Differentiation by OverLoading in C++) facilitates the evaluation of first and higher derivatives of vector functions that are defined by computer programs written in C or C++. The resulting derivative evaluation routines may be called from C/C++, Fortran, or any other language that can be linked with C. Homepage: https://projects.coin-or.org/ADOL-C URL: https://projects.coin-or.org/ADOL-C<br /><br /><br /></div>
 |-
 | align="center" | [https://software.intel.com/intel-advisor-xe advisor]
 | align="center" | tools
-| align="center" | 2018.3, 2019.3, 2020.3
+| align="center" | 2020.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Vectorization Optimization and Thread Prototyping - Vectorize and thread code or performance dies - Easy workflow + data + tips = faster code faster - Prioritize, Prototype and Predict performance gain Homepage: https://software.intel.com/intel-advisor-xe URL: https://software.intel.com/intel-advisor-xe Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [http://afni.nimh.nih.gov/ afni]
 | align="center" | bio
-| align="center" | 20.3.05, 21.2.10, 22.1.12, 23.1.00, 23.1.08, 24.1.03, 20180404
+| align="center" | 20.3.05, 21.2.10, 22.1.12, 23.1.00, 23.1.08, 24.1.03
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. Homepage: http://afni.nimh.nih.gov/ Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. Homepage: http://afni.nimh.nih.gov/ URL: http://afni.nimh.nih.gov/ Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://www.alberta-fem.de/ alberta]
-| align="center" | phys
-| align="center" | 3.0.3
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ALBERTA is an Adaptive multiLevel finite element toolbox using Bisectioning refinement and Error control by Residual Techniques for scientific Applications. Currently, ALBERTA works without problems on Linux PCs, DEC, HP, SGI, and SUN workstations. OpenGL (e.g. Mesa) is a plus, BLAS is a must. ALBERTA is freely distributed for research and education. Homepage: http://www.alberta-fem.de/ Keyword:phys<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/COMBINE-lab/alevin-fry alevin-fry]
@@ Line 69: / Line 64: @@
 | align="center" | 0.8.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding. Homepage: https://github.com/COMBINE-lab/alevin-fry URL: https://github.com/COMBINE-lab/alevin-fry<br /><br /><br /></div>
-|-
-| align="center" | [http://www.broadinstitute.org/software/allpaths-lg/blog/ allpaths-lg]
-| align="center" | bio
-| align="center" | 52488
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ALLPATHS-LG, the new short read genome assembler. Homepage: http://www.broadinstitute.org/software/allpaths-lg/blog/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/ttadano/ALM alm]
@@ Line 90: / Line 80: @@
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The ALPSCore project, based on the ALPS (Algorithms and Libraries for Physics Simulations) project, provides generic algorithms and utilities for physics problems. It strives to increase software reuse in the physics community. For copyright see COPYRIGHT.TXT For licensing see LICENSE.TXT For acknowledgment in scientific publications see ACKNOWLEDGE.TXT Homepage: https://github.com/ALPSCore/ALPSCore URL: https://github.com/ALPSCore/ALPSCore Keyword:phys<br /><br /><br /></div>
 |-
-| align="center" | [https://ambermd.org/amber.html amber]
+| align="center" | [http://ambermd.org/amber.html amber]
 | align="center" | chem
-| align="center" | 18.10-18.11, 18.14-18.17, 20.9-20.15, 20.12-20.15, 22.5-23.5
+| align="center" | 20.12-20.15, 18.14-18.17, 20.9-20.15, 22.5-23.5
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. Homepage: https://ambermd.org/amber.html URL: https://ambermd.org/amber.html Keyword:chem<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. Homepage: http://ambermd.org/amber.html URL: http://ambermd.org/amber.html Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://ambermd.org/AmberTools.php ambertools]
@@ Line 117: / Line 107: @@
 | align="center" | [http://www.popgen.dk/angsd angsd]
 | align="center" | bio
-| align="center" | 0.918, 0.929, 0.933, 0.935, 0.936, 0.939, 0.940
+| align="center" | 0.933, 0.935, 0.936, 0.939, 0.940
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Program for analysing NGS data. Homepage: http://www.popgen.dk/angsd URL: http://www.popgen.dk/angsd Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://annovar.openbioinformatics.org/en/latest/ annovar]
 | align="center" | bio
-| align="center" | 2017Jul16, 20191024
+| align="center" | 20191024
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others). Homepage: http://annovar.openbioinformatics.org/en/latest/ URL: http://annovar.openbioinformatics.org/en/latest/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 132: / Line 122: @@
 | align="center" | [http://www.ansys.com ansys]
 | align="center" | phys
-| align="center" | 16.2.3, 17.2, 18.1, 18.2, 19.1, 19.2, 2019R2, 2019R3, 2020R1, 2020R2, 2021R1, 2021R2, 2022R1, 2022R2, 2023R1, 2023R2
+| align="center" | 2019R3, 2020R2, 2021R1, 2021R2, 2022R1, 2022R2, 2023R1, 2023R2
 | Documentation: [[Ansys]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. Homepage: http://www.ansys.com URL: http://www.ansys.com Keyword:phys<br /><br /><br /></div>
 |-
@@ Line 152: / Line 142: @@
 | align="center" | [https://stnava.github.io/ANTs/ ants]
 | align="center" | vis
-| align="center" | 2.2.0, 2.3.2, 2.3.5, 2.4.4, 2.5.0
+| align="center" | 2.3.2, 2.3.5, 2.4.4, 2.5.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data. Homepage: https://stnava.github.io/ANTs/ URL: https://stnava.github.io/ANTs/ Keyword:vis<br /><br /><br /></div>
 |-
@@ Line 177: / Line 167: @@
 | align="center" | [https://github.com/bcgsc/arcs arcs]
 | align="center" | bio
-| align="center" | 1.0.1, 1.2.1, 1.2.5, 1.2.7
+| align="center" | 1.2.1, 1.2.5, 1.2.7
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data. Homepage: https://github.com/bcgsc/arcs URL: https://github.com/bcgsc/arcs Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 183: / Line 173: @@
 | align="center" | tools
 | align="center" | 2.13
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. Homepage: http://argtable.sourceforge.net/ Keyword:tools<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. Homepage: http://argtable.sourceforge.net/ URL: http://argtable.sourceforge.net/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://sourceforge.net/projects/actc arioc]
@@ Line 197: / Line 187: @@
 | align="center" | [https://arma.sourceforge.net/ armadillo]
 | align="center" | math
-| align="center" | 7.950.1, 8.500.1, 9.850.1, 9.900.2, 12.6.4
+| align="center" | 9.900.2, 12.6.4
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Homepage: https://arma.sourceforge.net/ URL: https://arma.sourceforge.net/ Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/opencollab/arpack-ng arpack-ng]
 | align="center" | math
-| align="center" | 3.5.0, 3.7.0, 3.8.0, 3.9.0, 3.9.1
+| align="center" | 3.7.0, 3.8.0, 3.9.0, 3.9.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. Homepage: https://github.com/opencollab/arpack-ng URL: https://github.com/opencollab/arpack-ng Keyword:math<br /><br /><br /></div>
 |-
@@ Line 212: / Line 202: @@
 | align="center" | [https://arrow.apache.org arrow]
 | align="center" | tools
-| align="center" | 0.11.1, 0.15.1, 0.16.0, 0.17.1, 1.0.0, 2.0.0, 5.0.0, 7.0.0, 8.0.0, 9.0.0, 10.0.1, 11.0.0, 12.0.1, 13.0.0, 14.0.0, 14.0.1, 15.0.1, 16.1.0
+| align="center" | 0.16.0, 0.17.1, 2.0.0, 5.0.0, 7.0.0, 8.0.0, 9.0.0, 10.0.1, 11.0.0, 12.0.1, 13.0.0, 14.0.0, 14.0.1, 15.0.1, 16.1.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Apache Arrow is a cross-language development platform for in-memory data. Homepage: https://arrow.apache.org URL: https://arrow.apache.org Compatible modules: python/3.11, python/3.10 Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 218: / Line 208: @@
 | align="center" | tools
 | align="center" | 3.5.4
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Aspera ASCP is a high speed file transfer software Homepage: http://downloads.asperasoft.com/ Keyword:tools<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Aspera ASCP is a high speed file transfer software Homepage: http://downloads.asperasoft.com/ URL: http://downloads.asperasoft.com/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://aspect.geodynamics.org/ aspect]
 | align="center" | -
-| align="center" | 2.1.0, 2.4.0
+| align="center" | 2.4.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ASPECT: Advanced Solver for Problems in Earth's ConvecTion. An extensible code written in C++ to support research in simulating convection in the Earth's mantle and elsewhere to provide the geosciences with a well-documented and extensible code base for their research needs and to create an open, inclusive, participatory community providing users and developers with a state-of-the-art, comprehensive software that performs well while being simple to extend. Homepage: https://aspect.geodynamics.org/ URL: https://aspect.geodynamics.org/<br /><br /><br /></div>
 |-
 | align="center" | [http://assimp.sourceforge.net/ assimp]
 | align="center" | -
-| align="center" | 4.1.0, 5.0.0
+| align="center" | 5.0.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Open Asset Import Library (short name: Assimp) is a portable Open Source library to import various well-known 3D model formats in a uniform manner. The most recent version also knows how to export 3d files and is therefore suitable as a general-purpose 3D model converter. Homepage: http://assimp.sourceforge.net/ URL: http://assimp.sourceforge.net/<br /><br /><br /></div>
 |-
@@ Line 243: / Line 233: @@
 | align="center" | chem
 | align="center" | 4.2.7_2
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ATOM is the name of a program originally written (circa 1982) by Sverre Froyen at the University of California at Berkeley, modified starting in 1990 by Norman Troullier and Jose Luis Martins at the University of Minnesota, and currently maintained by Alberto Garcia, who added some features and made substantial structural changes to the April 1990 (5.0) Minnesota version while at Berkeley and elsewhere. Homepage: https://departments.icmab.es/leem/siesta/Pseudopotentials/Code/downloads.html Keyword:chem<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ATOM is the name of a program originally written (circa 1982) by Sverre Froyen at the University of California at Berkeley, modified starting in 1990 by Norman Troullier and Jose Luis Martins at the University of Minnesota, and currently maintained by Alberto Garcia, who added some features and made substantial structural changes to the April 1990 (5.0) Minnesota version while at Berkeley and elsewhere. Homepage: https://departments.icmab.es/leem/siesta/Pseudopotentials/Code/downloads.html URL: https://departments.icmab.es/leem/siesta/Pseudopotentials/Code/downloads.html Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [http://atomicrex.gitlab.io/atomicrex/ atomicrex]
@@ Line 257: / Line 247: @@
 | align="center" | [https://bioinf.uni-greifswald.de/augustus/ augustus]
 | align="center" | bio
-| align="center" | 3.3.2, 3.3.3, 3.4.0, 3.5.0
+| align="center" | 3.3.3, 3.4.0, 3.5.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences Homepage: https://bioinf.uni-greifswald.de/augustus/ URL: https://bioinf.uni-greifswald.de/augustus/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 283: / Line 273: @@
 | align="center" | bio
 | align="center" | 2.5.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of lineage diversification and trait evolution. Homepage: http://bamm-project.org/ Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of lineage diversification and trait evolution. Homepage: http://bamm-project.org/ URL: http://bamm-project.org/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/pezmaster31/bamtools bamtools]
 | align="center" | bio
-| align="center" | 2.4.1, 2.5.1, 2.5.2
+| align="center" | 2.5.1, 2.5.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. Homepage: https://github.com/pezmaster31/bamtools URL: https://github.com/pezmaster31/bamtools Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 293: / Line 283: @@
 | align="center" | bio
 | align="center" | 1.0.14
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam. Homepage: http://genome.sph.umich.edu/wiki/BamUtil Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam. Homepage: http://genome.sph.umich.edu/wiki/BamUtil URL: http://genome.sph.umich.edu/wiki/BamUtil Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://sourceforge.net/projects/seqbarracuda/ barracuda]
@@ Line 308: / Line 298: @@
 | align="center" | bio
 | align="center" | 3.0.4
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes Homepage: http://www.rannala.org/?page_id=245 Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes Homepage: http://www.rannala.org/?page_id=245 URL: http://www.rannala.org/?page_id=245 Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://www.rannala.org/inference-of-recent-migration bayesass3-snps]
@@ Line 327: / Line 317: @@
 | align="center" | [https://bazel.io/ bazel]
 | align="center" | tools
-| align="center" | 0.5.2, 0.7.0, 0.11.1, 0.19.2, 0.25.2, 0.27.0, 3.6.0
+| align="center" | 3.6.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software. Homepage: https://bazel.io/ URL: https://bazel.io/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://sourceforge.net/projects/bbmap/ bbmap]
 | align="center" | bio
-| align="center" | 37.36, 37.78, 38.86, 39.06
+| align="center" | 37.78, 38.86, 39.06
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BBMap short read aligner, and other bioinformatic tools. Homepage: https://sourceforge.net/projects/bbmap/ URL: https://sourceforge.net/projects/bbmap/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 357: / Line 347: @@
 | align="center" | [https://github.com/beagle-dev/beagle-lib beagle-lib]
 | align="center" | bio
-| align="center" | 2.1.2, 3.1.1, 3.1.2, 4.0.0, 4.0.1
+| align="center" | 3.1.2, 4.0.0, 4.0.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. Homepage: https://github.com/beagle-dev/beagle-lib URL: https://github.com/beagle-dev/beagle-lib Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://beast2.org beast]
 | align="center" | bio
-| align="center" | 1.8.2, 2.4.0, 2.6.0, 2.6.2, 2.6.3, 2.7.5
+| align="center" | 2.6.3, 2.7.5
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. Homepage: http://beast2.org URL: http://beast2.org Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://bedops.readthedocs.io/en/latest/index.html bedops]
 | align="center" | -
-| align="center" | 2.4.35, 2.4.39, 2.4.41
+| align="center" | 2.4.39, 2.4.41
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster. Homepage: http://bedops.readthedocs.io/en/latest/index.html URL: http://bedops.readthedocs.io/en/latest/index.html<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/arq5x/bedtools2 bedtools]
 | align="center" | bio
-| align="center" | 2.27.1, 2.28.0, 2.29.2, 2.30.0, 2.31.0
+| align="center" | 2.29.2, 2.30.0, 2.31.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Homepage: https://github.com/arq5x/bedtools2 URL: https://github.com/arq5x/bedtools2 Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 382: / Line 372: @@
 | align="center" | [https://arxiv.org/abs/1111.4429). berkeleygw]
 | align="center" | phys
-| align="center" | 1.2.0, 2.1.0, 3.0.1, 4.0
+| align="center" | 2.1.0, 3.0.1, 4.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules. We ask that you please cite the following papers when using results obtained from the BerkeleyGW package: - Mark S. Hybertsen and Steven G. Louie, Electron correlation in semiconductors and insulators: Band gaps and quasiparticle energies, Phys. Rev. B 34, 5390 (1986). - Michael Rohlfing and Steven G. Louie, Electron-hole excitations and optical spectra from first principles, Phys. Rev. B 62, 4927 (2000). - Jack Deslippe, Georgy Samsonidze, David A. Strubbe, Manish Jain, Marvin L. Cohen, and Steven G. Louie, BerkeleyGW: A Massively Parallel Computer Package for the Calculation of the Quasiparticle and Optical Properties of Materials and Nanostructures, Comput. Phys. Commun. 183, 1269 (2012) (https://arxiv.org/abs/1111.4429). Homepage: http://www.berkeleygw.org URL: http://www.berkeleygw.org Keyword:phys<br /><br /><br /></div>
 |-
@@ Line 388: / Line 378: @@
 | align="center" | -
 | align="center" | 1.03
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: bgc implements Bayesian estimation of genomic clines to quantify introgression at many loci. Models are available for linked loci, genotype uncertainty and sequence errors. Models for genotype uncertainty and sequence error can be used to estimate genomic cline parameters from next-generation sequence data. Homepage: https://sites.google.com/site/bgcsoftware/<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: bgc implements Bayesian estimation of genomic clines to quantify introgression at many loci. Models are available for linked loci, genotype uncertainty and sequence errors. Models for genotype uncertainty and sequence error can be used to estimate genomic cline parameters from next-generation sequence data. Homepage: https://sites.google.com/site/bgcsoftware/ URL: https://sites.google.com/site/bgcsoftware/<br /><br /><br /></div>
-|-
-| align="center" | [https://bitbucket.org/gavinband/bgen/src/default/ bgen]
-| align="center" | -
-| align="center" | 1.1.4
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Reference implementation of the bgen format Homepage: https://bitbucket.org/gavinband/bgen/src/default/ URL: https://bitbucket.org/gavinband/bgen/src/default/<br /><br /><br /></div>
 |-
 | align="center" | [https://enkre.net/cgi-bin/code/bgen bgen-lib]
@@ Line 402: / Line 387: @@
 | align="center" | [http://bigdft.org/Wiki/index.php?title=BigDFT_website bigdft]
 | align="center" | chem
-| align="center" | 1.7.6, 1.8.3
+| align="center" | 1.8.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BigDFT is a DFT massively parallel electronic structure code using a wavelet basis set with the capability to use a linear scaling method. Wavelets form a real space basis set distributed on an adaptive mesh (two levels of resolution in our implementation). GTH or HGH pseudopotentials are used to remove the core electrons. The code BigDFT is available in ABINIT v5.5 and higher but can also be downloaded in a standalone version from the website. Thanks to our Poisson solver based on a Green function formalism, periodic systems, surfaces and isolated systems can be simulated with explicit boundary conditions. The Poisson solver can also be downloaded and used independently and is integrated in ABINIT, Octopus and CP2K. The code is free software, available under GNU-GPL license and the BigDFT developer community encourages anyone willing to contribute to join the team. Homepage: http://bigdft.org/Wiki/index.php?title=BigDFT_website URL: http://bigdft.org/Wiki/index.php?title=BigDFT_website Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 422: / Line 407: @@
 | align="center" | [https://bioperl.org/ bioperl]
 | align="center" | bio
-| align="center" | 1.7.1, 1.7.5, 1.7.7, 1.7.8
+| align="center" | 1.7.7, 1.7.8
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. Homepage: https://bioperl.org/ URL: https://bioperl.org/ Extensions: Bio::Procedural-1.7.4, BioPerl-1.7.8, XML::DOM::XPath-0.14, XML::Writer-0.900 Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 432: / Line 417: @@
 | align="center" | [http://www.bioinformatics.babraham.ac.uk/projects/bismark/ bismark]
 | align="center" | -
-| align="center" | 0.22.1, 0.22.3, 0.24.1
+| align="center" | 0.22.3, 0.24.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A tool to map bisulfite converted sequence reads and determine cytosine methylation states Homepage: http://www.bioinformatics.babraham.ac.uk/projects/bismark/ URL: http://www.bioinformatics.babraham.ac.uk/projects/bismark/<br /><br /><br /></div>
 |-
@@ Line 443: / Line 428: @@
 | align="center" | math
 | align="center" | 1.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The BLACS (Basic Linear Algebra Communication Subprograms) project is an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms. Homepage: http://www.netlib.org/blacs/ Keyword:math<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The BLACS (Basic Linear Algebra Communication Subprograms) project is an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms. Homepage: http://www.netlib.org/blacs/ URL: http://www.netlib.org/blacs/ Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/PacificBiosciences/blasr blasr]
 | align="center" | bio
-| align="center" | 5.3.0, 5.3.3
+| align="center" | 5.3.3
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The PacBioi long read aligner Homepage: https://github.com/PacificBiosciences/blasr URL: https://github.com/PacificBiosciences/blasr Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The PacBio long read aligner Homepage: https://github.com/PacificBiosciences/blasr URL: https://github.com/PacificBiosciences/blasr Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/PacificBiosciences/blasr_libcpp blasr_libcpp]
 | align="center" | bio
-| align="center" | 5.3.4, 20170426
+| align="center" | 5.3.4
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences Homepage: https://github.com/PacificBiosciences/blasr_libcpp Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences Homepage: https://github.com/PacificBiosciences/blasr_libcpp URL: https://github.com/PacificBiosciences/blasr_libcpp Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://blast.ncbi.nlm.nih.gov/ blast]
@@ Line 462: / Line 447: @@
 | align="center" | [https://blast.ncbi.nlm.nih.gov/ blast+]
 | align="center" | bio
-| align="center" | 2.7.1, 2.8.1, 2.9.0, 2.10.0, 2.10.1, 2.11.0, 2.12.0, 2.13.0, 2.14.1
+| align="center" | 2.10.1, 2.11.0, 2.12.0, 2.13.0, 2.14.1
 | Documentation: [[BLAST]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. Homepage: https://blast.ncbi.nlm.nih.gov/ URL: https://blast.ncbi.nlm.nih.gov/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 472: / Line 457: @@
 | align="center" | [https://www.blender.org/ blender]
 | align="center" | vis
-| align="center" | 2.79b, 2.92.0, 3.6.0, 4.0.2
+| align="center" | 2.92.0, 3.6.0, 4.0.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. Homepage: https://www.blender.org/ URL: https://www.blender.org/ Keyword:vis<br /><br /><br /></div>
 |-
@@ Line 482: / Line 467: @@
 | align="center" | [https://github.com/blitzpp/blitz blitz++]
 | align="center" | tools
-| align="center" | 1.0.1, 1.0.2
+| align="center" | 1.0.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ with a speed comparable to Fortran implementations, while preserving an object-oriented interface Homepage: https://github.com/blitzpp/blitz URL: https://github.com/blitzpp/blitz Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 502: / Line 487: @@
 | align="center" | [https://data.broadinstitute.org/alkesgroup/BOLT-LMM/ bolt-lmm]
 | align="center" | bio
-| align="center" | 2.2, 2.3.4, 2.4
+| align="center" | 2.3.4, 2.4
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The BOLT-LMM software package currently consists of two main algorithms, the BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML algorithm for variance components analysis (i.e., partitioning of SNP-heritability and estimation of genetic correlations). The BOLT-LMM algorithm computes statistics for testing association between phenotype and genotypes using a linear mixed model (LMM). The BOLT-REML algorithm estimates heritability explained by genotyped SNPs and genetic correlations among multiple traits measured on the same set of individuals. Like the GCTA software. Homepage: https://data.broadinstitute.org/alkesgroup/BOLT-LMM/ URL: https://data.broadinstitute.org/alkesgroup/BOLT-LMM/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 512: / Line 497: @@
 | align="center" | [https://www.boost.org/ boost]
 | align="center" | tools
-| align="center" | 1.54.0, 1.60.0, 1.65.1, 1.66.0, 1.68.0, 1.72.0, 1.76.0, 1.80.0, 1.82.0
+| align="center" | 1.72.0, 1.76.0, 1.80.0, 1.82.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: https://www.boost.org/ URL: https://www.boost.org/ Compatible modules: python/3.10, python/3.11 Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 522: / Line 507: @@
 | align="center" | [https://www.boost.org/ boost-mpi]
 | align="center" | tools
-| align="center" | 1.68.0, 1.72.0, 1.80.0, 1.82.0
+| align="center" | 1.72.0, 1.80.0, 1.82.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: https://www.boost.org/ URL: https://www.boost.org/ Compatible modules: python/3.10, python/3.11 Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [http://bowtie-bio.sourceforge.net/index.shtml bowtie]
 | align="center" | bio
-| align="center" | 1.1.2, 1.3.0
+| align="center" | 1.3.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome. Homepage: http://bowtie-bio.sourceforge.net/index.shtml URL: http://bowtie-bio.sourceforge.net/index.shtml Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml bowtie2]
 | align="center" | bio
-| align="center" | 2.3.4.3, 2.3.5, 2.3.5.1, 2.4.1, 2.4.2, 2.4.4, 2.5.1, 2.5.2, 2.5.4
+| align="center" | 2.4.1, 2.4.2, 2.4.4, 2.5.1, 2.5.2, 2.5.4
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml URL: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 539: / Line 524: @@
 | align="center" | 4.3.8, 4.6.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The aim of this project is to implement a versatile high-performance version of the BPP software. BPP implements four methods: * Estimation of the parameters of species divergence times and population sizes under the multi-species coalescent (MSC) model when the species phylogeny is given * Inference of the species tree when the assignments are given by the user * Species delimitation using a user-specified guide treed * Joint species delimitation and species tree estimation Homepage: https://github.com/bpp/bpp URL: https://github.com/bpp/bpp<br /><br /><br /></div>
-|-
-| align="center" | [http://biopp.univ-montp2.fr/wiki/index.php/Main_Page bpp-core]
-| align="center" | bio
-| align="center" | 2.4.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://biopp.univ-montp2.fr/wiki/index.php/Main_Page bpp-phyl]
-| align="center" | bio
-| align="center" | 2.4.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://biopp.univ-montp2.fr/wiki/index.php/Main_Page bpp-phyl-omics]
-| align="center" | bio
-| align="center" | 2.4.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://biopp.univ-montp2.fr/wiki/index.php/Main_Page bpp-popgen]
-| align="center" | bio
-| align="center" | 2.4.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://biopp.univ-montp2.fr/wiki/index.php/Main_Page bpp-seq]
-| align="center" | bio
-| align="center" | 2.4.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://biopp.univ-montp2.fr/wiki/index.php/Main_Page bpp-seq-omics]
-| align="center" | bio
-| align="center" | 2.4.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://ccb.jhu.edu/software/bracken/ bracken]
 | align="center" | -
-| align="center" | 2.5, 2.6.0, 2.7
+| align="center" | 2.6.0, 2.7
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is identical to other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. Combined with the Kraken classifier, Bracken produces accurate species- and genus-level abundance estimates even when a sample contains two or more near-identical species. NOTE: Bracken is compatible with both Kraken 1 and Kraken 2. However, the default kmer length is different depending on the version of Kraken used. If you use Kraken 1 defaults, specify 31 as the kmer length. If you use Kraken 2 defaults, specify 35 as the kmer length. Homepage: https://ccb.jhu.edu/software/bracken/ URL: https://ccb.jhu.edu/software/bracken/<br /><br /><br /></div>
-|-
-| align="center" | [http://gmt.genome.wustl.edu/packages/breakdancer breakdancer]
-| align="center" | bio
-| align="center" | 1.4.5
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads Homepage: http://gmt.genome.wustl.edu/packages/breakdancer Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://barricklab.org/breseq breseq]
 | align="center" | -
-| align="center" | 0.33.2, 0.35.2, 0.36.1, 0.38.2
+| align="center" | 0.35.2, 0.36.1, 0.38.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: breseq is a computational pipeline for the analysis of short-read re-sequencing data Homepage: https://barricklab.org/breseq URL: https://barricklab.org/breseq<br /><br /><br /></div>
 |-
@@ Line 607: / Line 557: @@
 | align="center" | [https://www.emc.ncep.noaa.gov/index.php?branch=BUFRLIB bufrlib]
 | align="center" | geo
-| align="center" | 10.2.3, 11.3.0.2
+| align="center" | 11.3.0.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NCEP BUFRLIB software to encode or decode BUFR messages. It is not intended to be a primer on the BUFR code form itself. Homepage: https://www.emc.ncep.noaa.gov/index.php?branch=BUFRLIB URL: https://www.emc.ncep.noaa.gov/index.php?branch=BUFRLIB Keyword:geo<br /><br /><br /></div>
 |-
 | align="center" | [http://bulletphysics.org/ bullet]
 | align="center" | -
-| align="center" | 2.88, 2.89, 3.24
+| align="center" | 2.89, 3.24
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bullet professional 3D Game Multiphysics Library provides state of the art collision detection, soft body and rigid body dynamics. Homepage: http://bulletphysics.org/ URL: http://bulletphysics.org/ Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: pybullet-3.2.4<br /><br /><br /></div>
-|-
-| align="center" | [https://busco.ezlab.org/ busco]
-| align="center" | bio
-| align="center" | 3.0.2, 5.2.2
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs Homepage: https://busco.ezlab.org/ URL: https://busco.ezlab.org/ Extensions: biopython-1.79, DendroPy-4.5.1, sepp-4.5.1 Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/BUStools/bustools bustools]
 | align="center" | -
-| align="center" | 0.39.2, 0.40.0
+| align="center" | 0.40.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. See the kallisto bustools website for examples and instructions on how to use bustools as part of a single-cell RNA-seq workflow. Homepage: https://github.com/BUStools/bustools URL: https://github.com/BUStools/bustools<br /><br /><br /></div>
 |-
 | align="center" | [http://bio-bwa.sourceforge.net/ bwa]
 | align="center" | bio
-| align="center" | 0.7.15, 0.7.17, 0.7.18
+| align="center" | 0.7.17, 0.7.18
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. Homepage: http://bio-bwa.sourceforge.net/ URL: http://bio-bwa.sourceforge.net/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 639: / Line 584: @@
 | align="center" | 1.9.14
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces. Homepage: https://core.tcl-lang.org/bwidget/home URL: https://core.tcl-lang.org/bwidget/home<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/christopherpoole/CADMesh cadmesh]
-| align="center" | -
-| align="center" | 1.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Importing predefined CAD models into GEANT4 is not always possible or requires intermediate file format conversion to Geometry Description Markup Language (GDML) using commercial or third party software. CADMesh is a direct CAD model import interface for GEANT4 leveraging ASSIMP for reading the CAD files. Homepage: https://github.com/christopherpoole/CADMesh<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/hahnlab/CAFE5 cafe5]
@@ Line 652: / Line 592: @@
 | align="center" | [https://github.com/Cantera/cantera cantera]
 | align="center" | chem
-| align="center" | 2.4.0, 2.5.1, 2.6.0
+| align="center" | 2.5.1, 2.6.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Chemical kinetics, thermodynamics, and transport tool suite Homepage: https://github.com/Cantera/cantera URL: https://github.com/Cantera/cantera Compatible modules: python/3.8, python/3.9, python/3.10 Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/marbl/canu canu]
 | align="center" | bio
-| align="center" | 1.8, 1.9, 2.0, 2.1.1, 2.2
+| align="center" | 2.0, 2.1.1, 2.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II or Oxford Nanopore MinION). Canu is a hierarchical assembly pipeline which runs in four steps: Detect overlaps in high-noise sequences using MHAP Generate corrected sequence consensus Trim corrected sequences Assemble trimmed corrected sequences Homepage: https://github.com/marbl/canu URL: https://github.com/marbl/canu Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/Illumina/canvas canvas]
-| align="center" | bio
-| align="center" | 1.25
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Canvas is a tool for calling copy number variants (CNVs) from human DNA sequencing data. It can work either with germline data, or paired tumor/normal samples. Its primary input is aligned reads (in .bam format), and its primary output is a report (in a .vcf file) giving the copy number status of the genome. To run, do mono $EBROOTCANVAS/Canvas.dll ... Homepage: https://github.com/Illumina/canvas Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://seq.cs.iastate.edu/ cap3]
 | align="center" | bio
 | align="center" | 20151002
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CAP3 assembly program Homepage: http://seq.cs.iastate.edu/ Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CAP3 assembly program Homepage: http://seq.cs.iastate.edu/ URL: http://seq.cs.iastate.edu/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://capnproto.org capnproto]
 | align="center" | -
 | align="center" | 0.7.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Capn Proto is an insanely fast data interchange format and capability-based RPC system. Homepage: https://capnproto.org URL: https://capnproto.org<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Cap'n Proto is an insanely fast data interchange format and capability-based RPC system. Homepage: https://capnproto.org URL: https://capnproto.org<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/casadi/casadi casadi]
@@ Line 679: / Line 614: @@
 | align="center" | 3.6.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CasADi is an open-source tool for nonlinear optimization and algorithmic differentiation. Homepage: https://github.com/casadi/casadi URL: https://github.com/casadi/casadi Compatible modules: python/3.8, python/3.9, python/3.10, python/3.11<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/prisms-center/CASMcode casm]
-| align="center" | chem
-| align="center" | 0.2.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CASM is an open source software package designed to perform first-principles statistical mechanical studies of multi-component crystalline solids. CASM interfaces with first-principles electronic structure codes, automates the construction and parameterization of effective Hamiltonians and subsequently builds highly optimized (kinetic) Monte Carlo codes to predict finite-temperature thermodynamic and kinetic properties. CASM uses group theoretic techniques that take full advantage of crystal symmetry in order to rigorously construct effective Hamiltonians for almost arbitrary degrees of freedom in crystalline solids. This includes cluster expansions for configurational disorder in multi-component solids and lattice-dynamical effective Hamiltonians for vibrational degrees of freedom involved in structural phase transitions. Homepage: https://github.com/prisms-center/CASMcode Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [http://best.snu.ac.kr/casper/ casper]
@@ Line 703: / Line 633: @@
 | align="center" | geo
 | align="center" | 4_0_a02
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Community Climate System Model (CCSM) is a coupled climate model for simulating the earth's climate system. Composed of four separate models simultaneously simulating the earth's atmosphere, ocean, land surface and sea-ice, and one central coupler component, the CCSM allows researchers to conduct fundamental research into the earth's past, present and future climate states. Homepage: http://www.cesm.ucar.edu/models/ccsm4.0/ Keyword:geo<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Community Climate System Model (CCSM) is a coupled climate model for simulating the earth's climate system. Composed of four separate models simultaneously simulating the earth's atmosphere, ocean, land surface and sea-ice, and one central coupler component, the CCSM allows researchers to conduct fundamental research into the earth's past, present and future climate states. Homepage: http://www.cesm.ucar.edu/models/ccsm4.0/ URL: http://www.cesm.ucar.edu/models/ccsm4.0/ Keyword:geo<br /><br /><br /></div>
 |-
 | align="center" | [http://weizhongli-lab.org/cd-hit/ cd-hit]
 | align="center" | bio
-| align="center" | 4.6.8, 4.8.1
+| align="center" | 4.8.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. Homepage: http://weizhongli-lab.org/cd-hit/ URL: http://weizhongli-lab.org/cd-hit/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 717: / Line 647: @@
 | align="center" | [https://code.zmaw.de/projects/cdo cdo]
 | align="center" | geo
-| align="center" | 1.7.2, 1.9.5, 1.9.8, 1.9.10, 2.0.4, 2.0.5, 2.2.2
+| align="center" | 1.9.8, 1.9.10, 2.0.4, 2.0.5, 2.2.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. Homepage: https://code.zmaw.de/projects/cdo URL: https://code.zmaw.de/projects/cdo Keyword:geo<br /><br /><br /></div>
 |-
@@ Line 723: / Line 653: @@
 | align="center" | bio
 | align="center" | 2.1.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Cell Ranger is a set of analysis pipelines that process Chromium single cell 3-RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. Cell Ranger 1.2 and later support libraries generated by the Chromium Single Cell 3i-v1 and v2 reagent kits, whereas Cell Ranger 1.1 and earlier do not support v2 libraries. Cell Ranger includes four main gene expression pipelines: - cellranger mkfastq wraps Illumina's bcl2fastq to correctly demultiplex Chromium-prepared sequencing samples and to convert barcode and read data to FASTQ files. - cellranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, and UMI counting. - cellranger aggr aggregates outputs from multiple runs of cellranger count, normalizing those runs to the same sequencing depth and then recomputing the gene-barcode matrices and analysis on the combined data. - cellranger reanalyze takes gene-barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using tunable parameter settings. These pipelines combine Chromium-specific algorithms with the widely used RNA-seq aligner STAR. Output is delivered in standard BAM, MEX, CSV, HDF5 and HTML formats that are augmented with cellular information. Homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Cell Ranger is a set of analysis pipelines that process Chromium single cell 3-RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. Cell Ranger 1.2 and later support libraries generated by the Chromium Single Cell 3i-v1 and v2 reagent kits, whereas Cell Ranger 1.1 and earlier do not support v2 libraries. Cell Ranger includes four main gene expression pipelines: - cellranger mkfastq wraps Illumina's bcl2fastq to correctly demultiplex Chromium-prepared sequencing samples and to convert barcode and read data to FASTQ files. - cellranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, and UMI counting. - cellranger aggr aggregates outputs from multiple runs of cellranger count, normalizing those runs to the same sequencing depth and then recomputing the gene-barcode matrices and analysis on the combined data. - cellranger reanalyze takes gene-barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using tunable parameter settings. These pipelines combine Chromium-specific algorithms with the widely used RNA-seq aligner STAR. Output is delivered in standard BAM, MEX, CSV, HDF5 and HTML formats that are augmented with cellular information. Homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome URL: https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/single-cell-genetics/cellsnp-lite cellsnp-lite]
@@ Line 732: / Line 662: @@
 | align="center" | [https://github.com/infphilo/centrifuge centrifuge]
 | align="center" | bio
-| align="center" | 1.0.4-beta
+| align="center" | 1.0.4-beta, 1.0.4
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: [Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers Homepage: https://github.com/infphilo/centrifuge URL: https://github.com/infphilo/centrifuge Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://uscilab.github.io/cereal/ cereal]
 | align="center" | -
-| align="center" | 1.2.2, 1.3.0, 1.3.2
+| align="center" | 1.3.0, 1.3.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone. Homepage: https://uscilab.github.io/cereal/ URL: https://uscilab.github.io/cereal/<br /><br /><br /></div>
 |-
@@ Line 747: / Line 677: @@
 | align="center" | [http://www.cesm.ucar.edu/models/cesm2/ cesm]
 | align="center" | geo
-| align="center" | 1_2_2, 2.1.1, 2.1.3
+| align="center" | 2.1.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Community Earth System Model (CESM) is a fully-coupled, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states. Homepage: http://www.cesm.ucar.edu/models/cesm2/ URL: http://www.cesm.ucar.edu/models/cesm2/ Keyword:geo<br /><br /><br /></div>
 |-
 | align="center" | [http://heasarc.gsfc.nasa.gov/fitsio/ cfitsio]
 | align="center" | vis
-| align="center" | 3.41, 3.42, 3.48, 3.49, 4.1.0, 4.3.0
+| align="center" | 3.41, 3.48, 3.49, 4.1.0, 4.3.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. Homepage: http://heasarc.gsfc.nasa.gov/fitsio/ URL: http://heasarc.gsfc.nasa.gov/fitsio/ Keyword:vis<br /><br /><br /></div>
 |-
@@ Line 762: / Line 692: @@
 | align="center" | [http://slater.chemie.uni-mainz.de/cfour/index.php?n=Main.Download cfour-mpi]
 | align="center" | chem
-| align="center" | 1.0, 2.1
+| align="center" | 2.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum chemical calculations on atoms and molecules. The major strength of the program suite is its rather sophisticated arsenal of high-level ab initio methods for the calculation of atomic and molecular properties. Virtually all approaches based on Muller-Plesset (MP) perturbation theory and the coupled-cluster approximation (CC) are available; most of these have complementary analytic derivative approaches within the package as well. CFOUR is not a commercial code. It is rather a program that is undergoing development; new techniques and improvements are constantly being made (mainly in the groups of John F. Stanton (until the end of 2016 at the University of Texas at Austin, USA, now at the Quantum Theory Project of the University of Florida at Gainesville, USA) and Juergen Gauss (Universitat Mainz, Germany)). For non-commercial purposes there is no charge to obtain CFOUR; one must simply sign a license agreement. http://slater.chemie.uni-mainz.de/cfour/index.php?n=Main.Download Homepage: http://www.cfour.de/ URL: http://www.cfour.de/ Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://www.cgal.org/ cgal]
 | align="center" | math
-| align="center" | 4.9, 4.14.3, 5.2.4, 5.5.2
+| align="center" | 4.14.3, 5.2.4, 5.5.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library. Homepage: https://www.cgal.org/ URL: https://www.cgal.org/ Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [https://cgns.github.io/ cgns]
 | align="center" | phys
-| align="center" | 3.3.1, 3.4.1, 4.1.0, 4.1.2
+| align="center" | 3.4.1, 4.1.0, 4.1.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The CGNS system is designed to facilitate the exchange of data between sites and applications, and to help stabilize the archiving of aerodynamic data. Homepage: https://cgns.github.io/ URL: https://cgns.github.io/ Keyword:phys<br /><br /><br /></div>
 |-
-| align="center" | [http://chaiscript.com/ chaiscript]
+| align="center" | [https://chapel-lang.org chapel-ofi]
-| align="center" | -
-| align="center" | 6.1.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ChaiScript is one of the only embedded scripting language designed from the ground up to directly target C++ and take advantage of modern C++ development techniques, working with the developer how they would expect it to work. Being a native C++ application, it has some advantages over existing embedded scripting languages: - It uses a header-only approach, which makes it easy to integrate with existing projects. - It maintains type safety between your C++ application and the user scripts. - It supports a variety of C++ techniques including callbacks, overloaded functions, class methods, and stl containers. Homepage: http://chaiscript.com/<br /><br /><br /></div>
-|-
-| align="center" | [https://chapel-lang.org chapel-ofi]
 | align="center" | -
 | align="center" | 1.31.0
@@ Line 797: / Line 722: @@
 | align="center" | [http://www.circos.ca/ circos]
 | align="center" | vis
-| align="center" | 0.69-6, 0.69-9
+| align="center" | 0.69-9
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Circos is a software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions. Homepage: http://www.circos.ca/ URL: http://www.circos.ca/ Keyword:vis<br /><br /><br /></div>
 |-
 | align="center" | [https://clang.llvm.org/ clang]
 | align="center" | tools
-| align="center" | 3.8.1, 3.9.0, 9.0.1, 11.0.0, 13.0.1, 17.0.6
+| align="center" | 9.0.1, 11.0.0, 13.0.1, 17.0.6
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. Homepage: https://clang.llvm.org/ URL: https://clang.llvm.org/ Compatible modules: python/3.10, python/3.11 Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://proj-clhep.web.cern.ch/proj-clhep/ clhep]
 | align="center" | math
-| align="center" | 2.4.1.0, 2.4.1.2, 2.4.1.3, 2.4.4.0, 2.4.6.2, 2.4.7.1
+| align="center" | 2.4.1.3, 2.4.4.0, 2.4.6.2, 2.4.7.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package. Homepage: https://proj-clhep.web.cern.ch/proj-clhep/ URL: https://proj-clhep.web.cern.ch/proj-clhep/ Keyword:math<br /><br /><br /></div>
 |-
@@ Line 813: / Line 738: @@
 | align="center" | bio
 | align="center" | 1.2.4
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms Homepage: http://www.clustal.org/omega/ Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms Homepage: http://www.clustal.org/omega/ URL: http://www.clustal.org/omega/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://www.cmake.org cmake]
 | align="center" | tools
-| align="center" | 3.12.3, 3.16.3, 3.18.4, 3.20.1, 3.21.4, 3.22.1, 3.23.1, 3.27.7
+| align="center" | 3.18.4, 3.20.1, 3.21.4, 3.22.1, 3.23.1, 3.27.7
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. Homepage: https://www.cmake.org URL: https://www.cmake.org Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 827: / Line 752: @@
 | align="center" | [https://github.com/cdr/code-server code-server]
 | align="center" | -
-| align="center" | 3.4.1, 3.5.0, 3.12.0
+| align="center" | 3.5.0, 3.12.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Run VS Code on any machine anywhere and access it in the browser. Homepage: https://github.com/cdr/code-server URL: https://github.com/cdr/code-server<br /><br /><br /></div>
 |-
@@ Line 847: / Line 772: @@
 | align="center" | [https://www.comsol.com comsol]
 | align="center" | phys
-| align="center" | 5.3a, 5.4, 5.5, 5.6, 6.0.0.405, 6.1, 6.1.0.357, 6.2.0.415
+| align="center" | 5.6, 6.0, 6.0.0.405, 6.1.0.357, 6.2, 6.2.0.415
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems. Homepage: https://www.comsol.com URL: https://www.comsol.com Keyword:phys<br /><br /><br /></div>
 |-
@@ Line 862: / Line 787: @@
 | align="center" | [https://github.com/Oshlack/Corset/wiki corset]
 | align="center" | bio
-| align="center" | 1.07, 1.09
+| align="center" | 1.09
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Corset is a command-line software program to go from a de novo transcriptome assembly to gene-level counts. Our software takes a set of reads that have been multi-mapped to the transcriptome (where multiple alignments per read were reported) and hierarchically clusters the transcripts based on the proportion of shared reads and expression patterns. It will report the clusters and gene-level counts for each sample, which are easily tested for differential expression with count based tools such as edgeR and DESeq. Homepage: https://github.com/Oshlack/Corset/wiki URL: https://github.com/Oshlack/Corset/wiki Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://www.cp2k.org/ cp2k]
 | align="center" | chem
-| align="center" | 4.1, 7.1, 8.2, 9.1
+| align="center" | 7.1, 8.2, 9.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. Homepage: https://www.cp2k.org/ URL: https://www.cp2k.org/ Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 874: / Line 799: @@
 | align="center" | 4.3
 | Documentation: [[CPMD]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. Homepage: http://cpmd.org URL: http://cpmd.org Keyword:chem<br /><br /><br /></div>
-|-
-| align="center" | [http://sourceforge.net/projects/cppunit/ cppunit]
-| align="center" | tools
-| align="center" | 1.12.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CppUnit is the C++ port of the famous JUnit framework for unit testing. Homepage: http://sourceforge.net/projects/cppunit/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/zeromq/cppzmq cppzmq]
@@ Line 897: / Line 817: @@
 | align="center" | [https://github.com/grimme-lab/crest crest]
 | align="center" | chem
-| align="center" | 2.10.1, 2.11, 2.12, 3.0.1
+| align="center" | 2.11, 2.12, 3.0.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Conformer-Rotamer Ensemble Sampling Tool Homepage: https://github.com/grimme-lab/crest URL: https://github.com/grimme-lab/crest Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [http://cromwell.readthedocs.io/ cromwell]
 | align="center" | tools
-| align="center" | 34, 58
+| align="center" | 58
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Scientific workflow engine designed for simplicity and scalability. Trivially transition between one off use cases to massive scale production environments http://cromwell.readthedocs.io/ Homepage: https://cromwell.readthedocs.io/ URL: https://cromwell.readthedocs.io/ Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 917: / Line 837: @@
 | align="center" | [https://www.cst.com/ cst]
 | align="center" | phys
-| align="center" | 2018, 2020
+| align="center" | 2020
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CST offers accurate, efficient computational solutions for electromagnetic design and analysis. CST simulation is user-friendly and enables users to choose the most appropriate method for the design and optimization of devices operating in a wide range of frequencies. Please note that we installed only Graphic frontend and command line interface. You need to provide your own license server in order to be able to run CST. Homepage: https://www.cst.com/ URL: https://www.cst.com/ Keyword:phys<br /><br /><br /></div>
 |-
@@ Line 957: / Line 877: @@
 | align="center" | [https://developer.nvidia.com/cuda-toolkit cuda]
 | align="center" | tools
-| align="center" | 7.5.18, 9.2.148, 10.0.130, 10.1, 10.2, 11.0, 11.1.1, 11.2.2, 11.4, 11.7, 11.8.0, 12.2
+| align="center" | 10.1, 10.2
 | Documentation: [[CUDA]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. Homepage: https://developer.nvidia.com/cuda-toolkit URL: https://developer.nvidia.com/cuda-toolkit Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://developer.nvidia.com/cudnn cudnn]
 | align="center" | math
-| align="center" | 7.4, 7.5, 7.6, 7.6.5, 8.0.3, 8.2.0, 8.6.0.163, 8.7.0.84, 8.9.5.29
+| align="center" | 8.0.3, 8.2.0, 8.6.0.163, 8.7.0.84, 8.9.5.29
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. Homepage: https://developer.nvidia.com/cudnn URL: https://developer.nvidia.com/cudnn Keyword:math<br /><br /><br /></div>
 |-
@@ Line 969: / Line 889: @@
 | align="center" | 2.2.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Transcript assembly, differential expression, and differential regulation for RNA-Seq Homepage: http://cole-trapnell-lab.github.io/cufflinks/ URL: http://cole-trapnell-lab.github.io/cufflinks/ Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [https://sourceforge.net/projects/cunit/ cunit]
-| align="center" | tools
-| align="center" | 2.1-3
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Automated testing framework for C. Homepage: https://sourceforge.net/projects/cunit/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://developer.nvidia.com/cuquantum-sdk cuquantum]
@@ Line 999: / Line 914: @@
 | align="center" | 1.2.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A genomic linkage feature visualization tools based on Perl. Homepage: https://sourceforge.net/projects/cvit/ URL: https://sourceforge.net/projects/cvit/ Extensions: Config::IniFiles-3.000002, Data::Dumper-2.173, ExtUtils::PkgConfig-1.16, GD-2.71, GD::Arrow-0.01, GD::SVG-0.33, GD::Text-0.86, SVG-2.84, Test::Fork-0.02<br /><br /><br /></div>
-|-
-| align="center" | [http://www.cwp.mines.edu/cwpcodes/ cwp_su]
-| align="center" | geo
-| align="center" | 44R11
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Seismic Unix is a seismic processing and research environment developed at the Center for Wave Phenomena. Homepage: http://www.cwp.mines.edu/cwpcodes/ Keyword:geo<br /><br /><br /></div>
 |-
 | align="center" | [https://dakota.sandia.gov/ dakota]
 | align="center" | tools
-| align="center" | 6.8, 6.13
+| align="center" | 6.13
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and UQ. Broadly, the Dakota software's advanced parametric analyses enable design exploration, model calibration, risk analysis, and quantification of margins and uncertainty with computational models. The Dakota toolkit provides a flexible, extensible interface between such simulation codes and its iterative systems analysis methods, which include: - optimization with gradient and nongradient-based methods; - uncertainty quantification with sampling, reliability, stochastic expansion, and epistemic methods; - parameter estimation using nonlinear least squares (deterministic) or Bayesian inference (stochastic); and - sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as hybrid optimization, surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. Homepage: https://dakota.sandia.gov/ URL: https://dakota.sandia.gov/ Keyword:tools<br /><br /><br /></div>
-|-
-| align="center" | [http://daltonprogram.org/ dalton]
-| align="center" | chem
-| align="center" | 2017-alpha, 2018
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Dalton suite consists of two separate executables, Dalton and LSDalton. The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory, whereas LSDalton is a linear-scaling HF and DFT code suitable for large molecular systems, now also with some CCSD capabilites. Any published work arising from use of one of the Dalton programs must acknowledge that by a proper reference. The following list of capabilities of the Dalton programs should give you some indication of whether or not the Dalton suite is able to meet your requirements.. Homepage: http://daltonprogram.org/ Keyword:chem<br /><br /><br /></div>
-|-
-| align="center" | [https://damask.mpie.de/Home/WebHome damask]
-| align="center" | -
-| align="center" | 2.0.3
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: DAMASK is a flexible and hierarchically structured model of material point behavior for the solution of elastoplastic boundary value problems along with damage and thermal physics. Homepage: https://damask.mpie.de/Home/WebHome URL: https://damask.mpie.de/Home/WebHome<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/cmks/DAS_Tool das_tool]
@@ Line 1,032: / Line 932: @@
 | align="center" | [https://github.com/rordenlab/dcm2niix dcm2niix]
 | align="center" | bio
-| align="center" | 1.0.20180622, 1.0.20200331, 1.0.20230411
+| align="center" | 1.0.20200331, 1.0.20230411
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. Homepage: https://github.com/rordenlab/dcm2niix URL: https://github.com/rordenlab/dcm2niix Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 1,042: / Line 942: @@
 | align="center" | [https://www.linaroforge.com ddt-cpu]
 | align="center" | tools
-| align="center" | 7.1, 18.3, 19.1.4, 20.2, 22.0.1, 23.1.1
+| align="center" | 20.2, 22.0.1, 23.1.1
 | Documentation: [[ARM software]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Profiler and debugger, combining MAP and DDT. Homepage: https://www.linaroforge.com URL: https://www.linaroforge.com<br /><br /><br /></div>
 |-
 | align="center" | [https://www.linaroforge.com ddt-gpu]
 | align="center" | tools
-| align="center" | 7.1, 18.3, 19.1.4, 20.2, 22.0.1, 23.1.1
+| align="center" | 20.2, 22.0.1, 23.1.1
 | Documentation: [[ARM software]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Profiler and debugger, combining MAP and DDT, with support for CUDA. Homepage: https://www.linaroforge.com URL: https://www.linaroforge.com<br /><br /><br /></div>
 |-
 | align="center" | [http://www.dealii.org/ dealii]
 | align="center" | math
-| align="center" | 8.5.0, 9.0.1, 9.2.0, 9.3.1
+| align="center" | 9.2.0, 9.3.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A C++ software library supporting the creation of finite element codes and an open community of users and developers. Homepage: http://www.dealii.org/ URL: http://www.dealii.org/ Keyword:math<br /><br /><br /></div>
-|-
-| align="center" | [http://www.dealii.org/ dealii-petsc]
-| align="center" | math
-| align="center" | 8.5.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A C++ software library supporting the creation of finite element codes and an open community of users and developers. Homepage: http://www.dealii.org/ Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [https://svn.oss.deltares.nl delft3d]
@@ Line 1,067: / Line 962: @@
 | align="center" | [https://github.com/dellytools/delly/ delly]
 | align="center" | -
-| align="center" | 0.7.8, 0.8.5, 1.1.6, 1.1.8
+| align="center" | 0.8.5, 1.1.6, 1.1.8
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. Homepage: https://github.com/dellytools/delly/ URL: https://github.com/dellytools/delly/<br /><br /><br /></div>
 |-
@@ Line 1,077: / Line 972: @@
 | align="center" | [https://www.dftb-plus.info dftbplus]
 | align="center" | chem
-| align="center" | 19.1, 21.1, 21.2
+| align="center" | 21.1, 21.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been developed for the DFTB framework so far. Using DFTB+ you can carry out quantum mechanical simulations like with ab-initio density functional theory based packages, but in an approximate way gaining typically around two order of magnitude in speed. Homepage: https://www.dftb-plus.info URL: https://www.dftb-plus.info Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/dftbplus/dftd3-lib dftd3-lib]
 | align="center" | chem
-| align="center" | 0.9, 0.10
+| align="center" | 0.10
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This is a repackaged version of the DFTD3 program by S. Grimme and his coworkers. The original program (V3.1 Rev 1) was downloaded at 2016-04-03. It has been converted to free format and encapsulated into modules. Homepage: https://github.com/dftbplus/dftd3-lib URL: https://github.com/dftbplus/dftd3-lib Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 1,092: / Line 987: @@
 | align="center" | [https://github.com/bbuchfink/diamond diamond]
 | align="center" | bio
-| align="center" | 0.8.38, 0.9.8, 0.9.14, 0.9.22, 0.9.32, 0.9.36, 2.0.2, 2.0.4, 2.0.9, 2.0.13, 2.0.15, 2.1.6, 2.1.7, 2.1.8
+| align="center" | 0.9.36, 2.0.4, 2.0.9, 2.0.13, 2.0.15, 2.1.6, 2.1.7, 2.1.8
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Accelerated BLAST compatible local sequence aligner Homepage: https://github.com/bbuchfink/diamond URL: https://github.com/bbuchfink/diamond Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 1,099: / Line 994: @@
 | align="center" | 21.1, 23.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations Homepage: http://www.diracprogram.org URL: http://www.diracprogram.org<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/GATB/DiscoSnp discosnp]
-| align="center" | bio
-| align="center" | 2.3.X
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads. The number of input read sets is not constrained, it can be one, two, or more. No reference genome is needed. Homepage: https://github.com/GATB/DiscoSnp Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [https://software.broadinstitute.org/software/discovar/blog/?page_id=98 discovardenovo]
-| align="center" | bio
-| align="center" | 52488
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: DISCOVAR de novo is a short read genome assembly developed by the Broad Institute. It can generate high quality assemblies from the latest 250 base Illumina paired-end PCR-free fragment read' Homepage: https://software.broadinstitute.org/software/discovar/blog/?page_id=98 Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://gitlab.com/dl_monte dl_monte]
@@ Line 1,117: / Line 1,002: @@
 | align="center" | [http://www.scd.stfc.ac.uk/SCD/44516.aspx dl_poly4]
 | align="center" | chem
-| align="center" | 4.08, 4.10.0
+| align="center" | 4.10.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith. Homepage: http://www.scd.stfc.ac.uk/SCD/44516.aspx URL: http://www.scd.stfc.ac.uk/SCD/44516.aspx Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 1,132: / Line 1,017: @@
 | align="center" | [https://www.microsoft.com/net/ dotnet-core]
 | align="center" | -
-| align="center" | 3.0.0, 3.1.8, 5.0.12, 6.0.0
+| align="center" | 3.1.8, 5.0.12, 6.0.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: .NET is a free, cross-platform, open source developer platform for building many different types of applications. With .NET, you can use multiple languages, editors, and libraries to build for web, mobile, desktop, gaming, and IoT. Contains the SDK and the Runtime. Homepage: https://www.microsoft.com/net/ URL: https://www.microsoft.com/net/<br /><br /><br /></div>
-|-
-| align="center" | [https://www.microsoft.com/net/ dotnet-core-runtime]
-| align="center" | tools
-| align="center" | 1.1.8, 2.0.7
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: .NET is a free, cross-platform, open source developer platform for building many different types of applications. Homepage: https://www.microsoft.com/net/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/google/double-conversion double-conversion]
@@ Line 1,167: / Line 1,047: @@
 | align="center" | [https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home eccodes]
 | align="center" | geo
-| align="center" | 2.8.2, 2.15.0, 2.18.0, 2.19.0, 2.22.1, 2.25.0, 2.31.0
+| align="center" | 2.15.0, 2.19.0, 2.22.1, 2.25.0, 2.31.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding). Homepage: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home URL: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home Compatible modules: python/3.10, python/3.11 Extensions: cfgrib-0.9.10.4, eccodes-1.6.1 Keyword:geo<br /><br /><br /></div>
-|-
-| align="center" | [https://www.perl.org/ eclipse]
-| align="center" | tools
-| align="center" | 4.6.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Eclipse is an integrated development environment (IDE) used in computer programming, and is the most widely used Java IDE.[6] It contains a base workspace and an extensible plug-in system for customizing the environment. Eclipse is written mostly in Java and its primary use is for developing Java applications, but it may also be used to develop applications in other programming languages via plug-ins, including: Ada, ABAP, C, C++, COBOL, D, Fortran, Haskell, JavaScript, Julia,[7] Lasso, Lua, NATURAL, Perl, PHP, Prolog, Python, R, Ruby (including Ruby on Rails framework), Rust, Scala, Clojure, Groovy, Scheme, and Erlang. It can also be used to develop documents with LaTeX (via a TeXlipse plug-in) and packages for the software Mathematica. Development environments include the Eclipse Java development tools (JDT) for Java and Scala, Eclipse CDT for C/C++, and Eclipse PDT for PHP, among others. - Homepage: https://www.perl.org/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://www.ncbi.nlm.nih.gov/books/NBK25501/ edirect]
@@ Line 1,179: / Line 1,054: @@
 | align="center" | 20.9.20231210
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases from a Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in a variety of formats. Homepage: https://www.ncbi.nlm.nih.gov/books/NBK25501/ URL: https://www.ncbi.nlm.nih.gov/books/NBK25501/<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/dipetkov/eems eems]
-| align="center" | bio
-| align="center" | 20171011
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This repository contains an implementation of the EEMS method for analyzing and visualizing spatial population structure from geo-referenced genetic samples. EEMS uses the concept of effective migration to model the relationship between genetics and geography, and it outputs an estimated effective migration surface (hence, EEMS) - a visual representation of population structure that can highlight potential regions of higher-than-average and lower-than-average historic gene flow. Homepage: https://github.com/dipetkov/eems Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://eigen.tuxfamily.org eigen]
 | align="center" | math
-| align="center" | 3.2.2, 3.2.10, 3.3.2, 3.3.5, 3.3.7, 3.4.0
+| align="center" | 3.3.7, 3.4.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. Homepage: https://eigen.tuxfamily.org URL: https://eigen.tuxfamily.org Keyword:math<br /><br /><br /></div>
 |-
@@ Line 1,193: / Line 1,063: @@
 | align="center" | bio
 | align="center" | 7.2.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker's variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Homepage: http://www.hsph.harvard.edu/alkes-price/software/ Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker's variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Homepage: http://www.hsph.harvard.edu/alkes-price/software/ URL: http://www.hsph.harvard.edu/alkes-price/software/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://elastix.isi.uu.nl/ elastix]
@@ Line 1,202: / Line 1,072: @@
 | align="center" | [https://elixir-lang.org/ elixir]
 | align="center" | tools
-| align="center" | 1.5, 1.13
+| align="center" | 1.13
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Elixir is a dynamic, functional language designed for building scalable and maintainable applications. Homepage: https://elixir-lang.org/ URL: https://elixir-lang.org/ Keyword:tools<br /><br /><br /></div>
-|-
-| align="center" | [http://elk.sourceforge.net/ elk]
-| align="center" | chem
-| align="center" | 5.2.14
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features. Written originally at Karl-Franzens-Universitt Graz as a milestone of the EXCITING EU Research and Training Network, the code is designed to be as simple as possible so that new developments in the field of density functional theory (DFT) can be added quickly and reliably. Homepage: http://elk.sourceforge.net/ Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://www.csc.fi/web/elmer elmerfem]
@@ Line 1,217: / Line 1,082: @@
 | align="center" | [https://elpa.mpcdf.mpg.de/ elpa]
 | align="center" | math
-| align="center" | 2017.11.001, 2018.11.001, 2020.05.001, 2023.05.001
+| align="center" | 2020.05.001, 2023.05.001
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Eigenvalue SoLvers for Petaflop-Applications. Homepage: https://elpa.mpcdf.mpg.de/ URL: https://elpa.mpcdf.mpg.de/ Keyword:math<br /><br /><br /></div>
-|-
-| align="center" | [https://wordpress.elsi-interchange.org/ elsi]
-| align="center" | -
-| align="center" | 2.2.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ELSI: ELectronic Structure Infrastructure is a software bundle and unified interface for methods that solve or circumvent eigenvalue problems in the self-consistent field cycle of density-functional theory. Homepage: https://wordpress.elsi-interchange.org/<br /><br /><br /></div>
-|-
-| align="center" | [http://emboss.sourceforge.net/ emboss]
-| align="center" | bio
-| align="center" | 6.6.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: EMBOSS is 'The European Molecular Biology Open Software Suite'. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. Homepage: http://emboss.sourceforge.net/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/embree/embree embree]
@@ Line 1,239: / Line 1,094: @@
 | align="center" | 9.3.0, 23.2.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: EnergyPlus is a whole building energy simulation program that engineers, architects, and researchers use to model both energy consumptionfor heating, cooling, ventilation, lighting and plug and process loadsand water use in buildings. Homepage: https://energyplus.net/downloads URL: https://energyplus.net/downloads<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/grimme-lab/enso enso]
-| align="center" | -
-| align="center" | 1.271
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Energetic sorting of conformer rotamer ensembles Homepage: https://github.com/grimme-lab/enso URL: https://github.com/grimme-lab/enso<br /><br /><br /></div>
-|-
-| align="center" | [http://www.utahresearch.org/mingfuzhu/erds/ erds]
-| align="center" | bio
-| align="center" | 1.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ERDS is an open-source software free to academia and nor-profit organization, designed for inferring copy number variants (CNVs) in high-coverage human genomes using next generation sequence (NGS) data. When a CNV presents in a test genome, multiple signatures, weak or strong, would present in the alignment data. ERDS starts from read depth (RD) information, and integrates other information including paired end mapping (PEM) and soft-clip signature to call CNVS sensitively and accurately. Homepage: http://www.utahresearch.org/mingfuzhu/erds/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://www.erlang.org/ erlangotp]
 | align="center" | tools
-| align="center" | 20.0, 23.3, 24.2
+| align="center" | 23.3, 24.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Erlang is a general-purpose concurrent, garbage-collected programming language and runtime system. Homepage: http://www.erlang.org/ URL: http://www.erlang.org/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://www.earthsystemcog.org/projects/esmf/ esmf]
 | align="center" | geo
-| align="center" | 7.1.0r, 8.0.1, 8.2.0, 8.4.0, 8.6.0
+| align="center" | 8.0.1, 8.2.0, 8.4.0, 8.6.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications. Homepage: https://www.earthsystemcog.org/projects/esmf/ URL: https://www.earthsystemcog.org/projects/esmf/ Compatible modules: python/3.10, python/3.11 Extensions: esmpy-8.6.0 Keyword:geo<br /><br /><br /></div>
 |-
@@ Line 1,275: / Line 1,120: @@
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. Homepage: http://www.etsf.eu/resources/software/libraries_and_tools URL: http://www.etsf.eu/resources/software/libraries_and_tools<br /><br /><br /></div>
 |-
-| align="center" | [http://www.ebi.ac.uk/~guy/exonerate/ exonerate]
+| align="center" | [https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate exonerate]
 | align="center" | bio
 | align="center" | 2.4.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. Homepage: http://www.ebi.ac.uk/~guy/exonerate/ Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. Homepage: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate URL: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://libexpat.github.io expat]
 | align="center" | tools
-| align="center" | 2.2.6, 2.2.9, 2.2.10, 2.4.1
+| align="center" | 2.2.9, 2.2.10, 2.4.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) Homepage: https://libexpat.github.io URL: https://libexpat.github.io Keyword:tools<br /><br /><br /></div>
-|-
-| align="center" | [https://pachterlab.github.io/eXpress express]
-| align="center" | -
-| align="center" | 1.5.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Streaming quantification for high-throughput sequencing Homepage: https://pachterlab.github.io/eXpress URL: https://pachterlab.github.io/eXpress<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/facebookresearch/faiss faiss]
 | align="center" | -
-| align="center" | 1.6.2, 1.6.5, 1.7.1, 1.7.3, 1.7.4, 1.8.0
+| align="center" | 1.6.5, 1.7.1, 1.7.3, 1.7.4, 1.8.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Faiss is a library for efficient similarity search and clustering of dense vectors. It contains algorithms that search in sets of vectors of any size, up to ones that possibly do not fit in RAM. It also contains supporting code for evaluation and parameter tuning. Faiss is written in C++ with complete wrappers for Python/numpy. Some of the most useful algorithms are implemented on the GPU. Homepage: https://github.com/facebookresearch/faiss URL: https://github.com/facebookresearch/faiss Compatible modules: python/3.10, python/3.11<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/PacificBiosciences/FALCON falcon]
-| align="center" | bio
-| align="center" | 1.8.8
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Falcon: a set of tools for fast aligning long reads for consensus and assembly Homepage: https://github.com/PacificBiosciences/FALCON Extensions: FALCON-1.8.8, networkx-1.10, pypeFLOW-20170504 Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://leenissen.dk fann]
@@ Line 1,305: / Line 1,140: @@
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Fast Artificial Neural Network Library is a free open source neural network library, which implements multilayer artificial neural networks in C with support for both fully connected and sparsely connected networks. Homepage: http://leenissen.dk URL: http://leenissen.dk<br /><br /><br /></div>
 |-
-| align="center" | [https://bitbucket.org/jerlar73/fast-gbs fast-gbs]
+| align="center" | [http://fasta.bioch.virginia.edu fasta]
-| align="center" | bio
-| align="center" | 2017-01-25
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A bioinformatic pipeline designed to extract a high-quality SNP catalog starting from FASTQ files obtained from sequencing genotyping-by-sequencing (GBS) libraries. Homepage: https://bitbucket.org/jerlar73/fast-gbs Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://fasta.bioch.virginia.edu fasta]
 | align="center" | bio
 | align="center" | 36.3.8h
@@ Line 1,322: / Line 1,152: @@
 | align="center" | [https://github.com/ParBLiSS/FastANI fastani]
 | align="center" | -
-| align="center" | 1.2, 1.3, 1.32
+| align="center" | 1.32
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Homepage: https://github.com/ParBLiSS/FastANI URL: https://github.com/ParBLiSS/FastANI<br /><br /><br /></div>
 |-
 | align="center" | [http://www.atgc-montpellier.fr/fastme/ fastme]
 | align="center" | bio
-| align="center" | 2.1.6.1, 2.1.6.2
+| align="center" | 2.1.6.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FastME: a comprehensive, accurate and fast distance-based phylogeny inference program. Homepage: http://www.atgc-montpellier.fr/fastme/ URL: http://www.atgc-montpellier.fr/fastme/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/OpenGene/fastp fastp]
 | align="center" | bio
-| align="center" | 0.19.5, 0.20.0, 0.20.1, 0.23.1, 0.23.4
+| align="center" | 0.20.1, 0.23.1, 0.23.4
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Homepage: https://github.com/OpenGene/fastp URL: https://github.com/OpenGene/fastp Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 1,357: / Line 1,187: @@
 | align="center" | [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ fastqc]
 | align="center" | bio
-| align="center" | 0.11.5, 0.11.8, 0.11.9, 0.12.0, 0.12.1
+| align="center" | 0.11.9, 0.12.0, 0.12.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline. Homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://fastqtl.sourceforge.net/ fastqtl]
-| align="center" | -
-| align="center" | 2.184
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FastQTL is a QTL mapper Homepage: http://fastqtl.sourceforge.net/ URL: http://fastqtl.sourceforge.net/<br /><br /><br /></div>
 |-
 | align="center" | [http://cmpg.unibe.ch/software/fastsimcoal2/ fastsimcoal2]
@@ Line 1,377: / Line 1,202: @@
 | align="center" | [http://www.microbesonline.org/fasttree/ fasttree]
 | align="center" | bio
-| align="center" | 2.1.10, 2.1.11
+| align="center" | 2.1.11
 | Documentation: [[FastTree]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. Homepage: http://www.microbesonline.org/fasttree/ URL: http://www.microbesonline.org/fasttree/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 1,389: / Line 1,214: @@
 | align="center" | 6.7.5, 6.7.6, 6.7.7, 6.7.8, 6.7.9, 6.8.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. Homepage: https://pages.nist.gov/fds-smv/ URL: https://pages.nist.gov/fds-smv/<br /><br /><br /></div>
-|-
-| align="center" | [https://altairhyperworks.com/product/FEKO feko]
-| align="center" | phys
-| align="center" | 2018
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FEKO is a comprehensive computational electromagnetics (CEM) code used widely in the telecommunications, automobile, space and defense industries. Homepage: https://altairhyperworks.com/product/FEKO Keyword:phys<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/lh3/fermi-lite fermi-lite]
@@ Line 1,407: / Line 1,227: @@
 | align="center" | [https://www.ffmpeg.org/ ffmpeg]
 | align="center" | -
-| align="center" | 4.2.1, 4.2.2, 4.3.2
+| align="center" | 4.2.2, 4.3.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A complete, cross-platform solution to record, convert and stream audio and video. Homepage: https://www.ffmpeg.org/ URL: https://www.ffmpeg.org/<br /><br /><br /></div>
 |-
 | align="center" | [https://www.fftw.org fftw]
 | align="center" | math
-| align="center" | 3.3.6, 3.3.7, 3.3.8, 3.3.10
+| align="center" | 3.3.8, 3.3.10
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. Homepage: https://www.fftw.org URL: https://www.fftw.org Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [https://www.fftw.org fftw-mpi]
 | align="center" | math
-| align="center" | 3.3.6, 3.3.8, 3.3.9, 3.3.10
+| align="center" | 3.3.8, 3.3.9, 3.3.10
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. Homepage: https://www.fftw.org URL: https://www.fftw.org Keyword:math<br /><br /><br /></div>
 |-
@@ Line 1,429: / Line 1,249: @@
 | align="center" | 0.2.0, 0.2.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter Homepage: https://github.com/rrwick/Filtlong URL: https://github.com/rrwick/Filtlong Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html fineradstructure]
-| align="center" | -
-| align="center" | 0.3.2r109
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The fineSTRUCTURE package represents a powerful model-based approach to investigating population structure using genetic data. Homepage: http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html URL: http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html<br /><br /><br /></div>
 |-
 | align="center" | [https://ccb.jhu.edu/software/FLASH/ flash]
@@ Line 1,444: / Line 1,259: @@
 | align="center" | 2.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter Homepage: https://github.com/gabraham/flashpca/ URL: https://github.com/gabraham/flashpca/<br /><br /><br /></div>
-|-
-| align="center" | [http://www.flapw.de/ flashpca2]
-| align="center" | -
-| align="center" | d891160a
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FlashPCA performs fast principal component analysis (PCA) of single nucleotide polymorphism (SNP) data. FlashPCA is based on the Spectra library. Homepage: http://www.flapw.de/ URL: http://www.flapw.de/<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/google/flatbuffers/ flatbuffers]
@@ Line 1,454: / Line 1,264: @@
 | align="center" | 22.9.24
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FlatBuffers: Memory Efficient Serialization Library Homepage: https://github.com/google/flatbuffers/ URL: https://github.com/google/flatbuffers/<br /><br /><br /></div>
-|-
-| align="center" | [http://www.flapw.de/ fleur]
-| align="center" | -
-| align="center" | MaX-R4
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FLEUR is a feature-full, freely available FLAPW (full potential linearized augmented planewave) code, based on density-functional theory. Homepage: http://www.flapw.de/ URL: http://www.flapw.de/<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/seqan/flexbar flexbar]
-| align="center" | -
-| align="center" | 3.5.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Flexbar flexible barcode and adapter removal: The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Several adapter removal presets for Illumina libraries are included. Flexbar computes exact overlap alignments using SIMD and multicore parallelism. Moreover, trimming and filtering features are provided, e.g. trimming of homopolymers at read ends. Flexbar increases read mapping rates and improves genome as well as transcriptome assemblies. Unique molecular identifiers can be extracted in a flexible way. The software supports data in fasta and fastq format from multiple sequencing platforms. Homepage: https://github.com/seqan/flexbar URL: https://github.com/seqan/flexbar<br /><br /><br /></div>
 |-
 | align="center" | [https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release flexiblas]
@@ Line 1,472: / Line 1,272: @@
 | align="center" | [http://www.flintlib.org/ flint]
 | align="center" | math
-| align="center" | 2.5.2, 2.7.1, 2.9.0, 3.0.0
+| align="center" | 2.7.1, 2.9.0, 3.0.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FLINT (Fast Library for Number Theory) is a C library in support of computations in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides various low-level routines for fast arithmetic. FLINT is extensively documented and tested. Homepage: http://www.flintlib.org/ URL: http://www.flintlib.org/ Keyword:math<br /><br /><br /></div>
-|-
-| align="center" | [https://www.ansys.com/products/fluids/ansys-fluent fluent]
-| align="center" | phys
-| align="center" | 16.1
-| Documentation: [[Ansys]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ANSYS Fluent software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications, ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants. Fluent covers a broad reach, including special models with capabilities to model in-cylinder combustion, aero-acoustics, turbomachinery and multiphase systems. Homepage: https://www.ansys.com/products/fluids/ansys-fluent Keyword:phys<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/HudsonAlpha/fmlrc2 fmlrc2]
@@ Line 1,497: / Line 1,292: @@
 | align="center" | [http://fmtlib.net/ fmt]
 | align="center" | -
-| align="center" | 5.3.0, 6.1.1, 6.2.1, 7.0.3, 9.1.0
+| align="center" | 5.3.0, 6.2.1, 7.0.3, 9.1.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: fmt (formerly cppformat) is an open-source formatting library. Homepage: http://fmtlib.net/ URL: http://fmtlib.net/<br /><br /><br /></div>
 |-
 | align="center" | [https://www.freepascal.org fpc]
 | align="center" | tools
-| align="center" | 3.0.0, 3.2.2
+| align="center" | 3.2.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Free Pascal is a mature, versatile, open source Pascal compiler. Homepage: https://www.freepascal.org URL: https://www.freepascal.org Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 1,513: / Line 1,308: @@
 | align="center" | bio
 | align="center" | 1.30, 1.31
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FragGeneScan is an application for finding (fragmented) genes in short reads. Homepage: http://omics.informatics.indiana.edu/FragGeneScan/ Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FragGeneScan is an application for finding (fragmented) genes in short reads. Homepage: http://omics.informatics.indiana.edu/FragGeneScan/ URL: http://omics.informatics.indiana.edu/FragGeneScan/ Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://grigoriefflab.janelia.org/frealign frealign]
-| align="center" | chem
-| align="center" | 9.11
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Frealign is a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles. Homepage: http://grigoriefflab.janelia.org/frealign Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/freebayes/freebayes freebayes]
 | align="center" | bio
-| align="center" | 1.1.0, 1.2.0, 1.3.6, 1.3.7
+| align="center" | 1.2.0, 1.3.6, 1.3.7
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. Homepage: https://github.com/freebayes/freebayes URL: https://github.com/freebayes/freebayes Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 1,537: / Line 1,327: @@
 | align="center" | [https://www.gaia-gis.it/fossil/freexl/index freexl]
 | align="center" | tools
-| align="center" | 1.0.3, 1.0.5, 2.0.0
+| align="center" | 1.0.5, 2.0.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet. Homepage: https://www.gaia-gis.it/fossil/freexl/index URL: https://www.gaia-gis.it/fossil/freexl/index Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://www.fmrib.ox.ac.uk/fsl/ fsl]
 | align="center" | bio
-| align="center" | 6.0.1, 6.0.3, 6.0.4, 6.0.7.7
+| align="center" | 6.0.3, 6.0.4, 6.0.7.7
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. Homepage: https://www.fmrib.ox.ac.uk/fsl/ URL: https://www.fmrib.ox.ac.uk/fsl/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 1,549: / Line 1,339: @@
 | align="center" | 20141119, 20151117
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A tiny C library for managing SOM (Self-Organizing Maps) neural networks. Homepage: https://github.com/ekg/fsom URL: https://github.com/ekg/fsom<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/ctSkennerton/fxtract fxtract]
-| align="center" | -
-| align="center" | 2.3
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Extract sequences from a fastx file given a subsequence or identifier Homepage: https://github.com/ctSkennerton/fxtract<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/NOAA-EMC/NCEPLIBS-g2c g2clib]
@@ Line 1,562: / Line 1,347: @@
 | align="center" | [https://github.com/NOAA-EMC/NCEPLIBS-g2/ g2lib]
 | align="center" | geo
-| align="center" | 1.4.0, 3.1.0, 3.4.8
+| align="center" | 3.1.0, 3.4.8
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Library contains GRIB2 encoder/decoder and search/indexing routines. Homepage: https://github.com/NOAA-EMC/NCEPLIBS-g2/ URL: https://github.com/NOAA-EMC/NCEPLIBS-g2/ Keyword:geo<br /><br /><br /></div>
 |-
 | align="center" | [http://hpc.pnl.gov/globalarrays/ ga]
 | align="center" | tools
-| align="center" | 5.7, 5.7.2
+| align="center" | 5.7.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model. It provides primitives for one-sided communication (Get, Put, Accumulate) and Atomic Operations (read increment). It supports blocking and non-blocking primtives, and supports location consistency. I8 version. Homepage: http://hpc.pnl.gov/globalarrays/ URL: http://hpc.pnl.gov/globalarrays/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://www.msg.chem.iastate.edu/GAMESS/GAMESS.html gamess-us]
 | align="center" | chem
-| align="center" | 20210930-R2P1, 2020.2, 20170420-R1, 20180920-R3, 20190630-R1, 20220930-R2, 20230630-R1, 20230930-R2
+| align="center" | 20210930-R2P1, 2020.2, 20220930-R2, 20230630-R1, 20230930-R2
 | Documentation: [[GAMESS-US]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. This version of GAMESS-US is built with Intel compilers, mixed DDI, and OpenMPI 4.1. Homepage: https://www.msg.chem.iastate.edu/GAMESS/GAMESS.html URL: https://www.msg.chem.iastate.edu/GAMESS/GAMESS.html Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 1,587: / Line 1,372: @@
 | align="center" | [http://www.broadinstitute.org/gatk/ gatk]
 | align="center" | bio
-| align="center" | 3.7, 3.8, 4.0.0.0, 4.0.8.1, 4.0.12.0, 4.1.0.0, 4.1.2.0, 4.1.7.0, 4.1.8.0, 4.1.8.1, 4.2.2.0, 4.2.4.0, 4.2.5.0, 4.4.0.0
+| align="center" | 4.1.8.0, 4.1.8.1, 4.2.2.0, 4.2.4.0, 4.2.5.0, 4.4.0.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Homepage: http://www.broadinstitute.org/gatk/ URL: http://www.broadinstitute.org/gatk/ Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://www.broadinstitute.org/gatk/ gatk-queue]
-| align="center" | bio
-| align="center" | 3.8-0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Homepage: http://www.broadinstitute.org/gatk/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://gazebosim.org gazebo]
@@ Line 1,607: / Line 1,387: @@
 | align="center" | [https://gcc.gnu.org/ gcc]
 | align="center" | tools
-| align="center" | 4.8.5, 4.9.4, 5.4.0, 6.4.0, 7.3.0, 8.3.0, 8.4.0, 9.1.0, 9.3.0, 10.2.0, 10.3.0, 11.3.0, 12.3, 13.3
+| align="center" | 8.4.0, 9.3.0, 10.2.0, 10.3.0, 11.3.0, 12.3, 13.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). Homepage: https://gcc.gnu.org/ URL: https://gcc.gnu.org/ Keyword:tools<br /><br /><br /></div>
-|-
-| align="center" | [http://gcc.gnu.org/ gcc-offload]
-| align="center" | -
-| align="center" | 7.3.0, 9.1.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The GNU Compiler with OpenMP/OpenACC offload support for Nvidia PTX Homepage: http://gcc.gnu.org/ URL: http://gcc.gnu.org/<br /><br /><br /></div>
 |-
 | align="center" | [http://gclust.c.u-tokyo.ac.jp/ gclust]
@@ Line 1,632: / Line 1,407: @@
 | align="center" | [https://www.gdal.org/ gdal]
 | align="center" | geo
-| align="center" | 2.1.3, 2.2.1, 2.4.1, 3.0.1, 3.0.4, 3.2.3, 3.4.1, 3.5.1, 3.7.2, 3.9.1
+| align="center" | 3.0.4, 3.2.3, 3.4.1, 3.5.1, 3.7.2, 3.9.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing. Homepage: https://www.gdal.org/ URL: https://www.gdal.org/ Compatible modules: python/3.10, python/3.10, python/3.11, python/3.11, python/3.12, python/3.12, python/3.10, python/3.10, python/3.11, python/3.11, python/3.12, python/3.12 Extensions: osgeo-3.9.1 Keyword:geo<br /><br /><br /></div>
 |-
@@ Line 1,642: / Line 1,417: @@
 | align="center" | [https://github.com/NVIDIA/gdrcopy gdrcopy]
 | align="center" | -
-| align="center" | 2.1, 2.3.1, 2.4.1
+| align="center" | 2.1, 2.3, 2.3.1, 2.4.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. Homepage: https://github.com/NVIDIA/gdrcopy URL: https://github.com/NVIDIA/gdrcopy<br /><br /><br /></div>
 |-
 | align="center" | [https://geant4.web.cern.ch/ geant4]
 | align="center" | phys
-| align="center" | 9.6.p04, 10.02.p03, 10.04.p02, 10.06, 10.7.3, 11.1.0, 11.1.2
+| align="center" | 10.06, 10.7.3, 11.1.0, 11.1.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science. Homepage: https://geant4.web.cern.ch/ URL: https://geant4.web.cern.ch/ Keyword:phys<br /><br /><br /></div>
 |-
@@ Line 1,672: / Line 1,447: @@
 | align="center" | [http://veda.cs.uiuc.edu/Seq2Expr/ gemma]
 | align="center" | bio
-| align="center" | 0.97, 0.98.3, 0.98.5
+| align="center" | 0.98.3, 0.98.5
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets. Homepage: http://veda.cs.uiuc.edu/Seq2Expr/ URL: http://veda.cs.uiuc.edu/Seq2Expr/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 1,687: / Line 1,462: @@
 | align="center" | [http://genometools.org genometools]
 | align="center" | bio
-| align="center" | 1.5.10, 1.6.1
+| align="center" | 1.6.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A comprehensive software library for efficient processing of structured genome annotations. Homepage: http://genometools.org URL: http://genometools.org Keyword:bio<br /><br /><br /></div>
+|-
+| align="center" | [https://wiki.gentoo.org/wiki/Project:Prefix gentoo]
+| align="center" | -
+| align="center" | 2020, 2023
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Gentoo prefix is Gentoo Linux installed in a prefix - Homepage: https://wiki.gentoo.org/wiki/Project:Prefix<br /><br /><br /></div>
 |-
 | align="center" | [https://www.geopsy.org/ geopsy]
@@ Line 1,697: / Line 1,477: @@
 | align="center" | [https://trac.osgeo.org/geos geos]
 | align="center" | geo
-| align="center" | 3.6.1, 3.7.2, 3.7.3, 3.8.1, 3.9.1, 3.10.2, 3.12.0
+| align="center" | 3.7.3, 3.8.1, 3.9.1, 3.10.2, 3.12.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) Homepage: https://trac.osgeo.org/geos URL: https://trac.osgeo.org/geos Keyword:geo<br /><br /><br /></div>
 |-
@@ Line 1,704: / Line 1,484: @@
 | align="center" | 20131206
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Gerris is a Free Software program for the solution of the partial differential equations describing fluid flow Homepage: http://gfs.sourceforge.net/wiki/index.php/Main_Page URL: http://gfs.sourceforge.net/wiki/index.php/Main_Page<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/gpertea/gffcompare gffcompare]
-| align="center" | -
-| align="center" | 0.11.6
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GffCompare provides classification and reference annotation mapping and matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files. Homepage: https://github.com/gpertea/gffcompare URL: https://github.com/gpertea/gffcompare<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/gpertea/gffread gffread]
@@ Line 1,719: / Line 1,494: @@
 | align="center" | 2.2.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used. Homepage: https://github.com/gflags/gflags URL: https://github.com/gflags/gflags<br /><br /><br /></div>
-|-
-| align="center" | [http://ghostscript.com ghostscript]
-| align="center" | -
-| align="center" | 9.26
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that. Homepage: http://ghostscript.com<br /><br /><br /></div>
 |-
 | align="center" | [https://aoterodelaroza.github.io/gibbs2/ gibbs2]
@@ Line 1,737: / Line 1,507: @@
 | align="center" | [http://git-annex.branchable.com/ git-annex]
 | align="center" | tools
-| align="center" | 6.20180807, 8.20200810, 10.20221003, 10.20231129
+| align="center" | 8.20200810, 10.20221003, 10.20231129
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: git-annex allows managing files with git, without checking the file contents into git. While that may seem paradoxical, it is useful when dealing with files larger than git can currently easily handle, whether due to limitations in memory, time, or disk space. Homepage: http://git-annex.branchable.com/ URL: http://git-annex.branchable.com/ Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 1,758: / Line 1,528: @@
 | align="center" | -
 | align="center" | 3.3.2, 3.3.8
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop Homepage: https://www.glfw.org URL: https://www.glfw.org Compatible modules: python/3.10, python/3.10, python/3.10, python/3.10, python/3.11, python/3.11, python/3.11, python/3.11 Extensions: glfw-2.6.2<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop Homepage: https://www.glfw.org URL: https://www.glfw.org<br /><br /><br /></div>
 |-
 | align="center" | [https://ccb.jhu.edu/software/glimmerhmm glimmerhmm]
@@ Line 1,772: / Line 1,542: @@
 | align="center" | [https://github.com/g-truc/glm glm]
 | align="center" | vis
-| align="center" | 0.9.7.2, 0.9.9.8
+| align="center" | 0.9.9.8
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications. Homepage: https://github.com/g-truc/glm URL: https://github.com/g-truc/glm Keyword:vis<br /><br /><br /></div>
 |-
@@ Line 1,787: / Line 1,557: @@
 | align="center" | [https://www.gnu.org/software/glpk/ glpk]
 | align="center" | math
-| align="center" | 4.61, 4.65, 5.0
+| align="center" | 4.65, 5.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library. Homepage: https://www.gnu.org/software/glpk/ URL: https://www.gnu.org/software/glpk/ Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [http://research-pub.gene.com/gmap/ gmap-gsnap]
 | align="center" | bio
-| align="center" | 2018-07-04, 2019-09-12, 2020-11-14
+| align="center" | 2020-11-14, 2019-09-12
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program Homepage: http://research-pub.gene.com/gmap/ URL: http://research-pub.gene.com/gmap/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://gmplib.org/ gmp]
 | align="center" | -
-| align="center" | 6.1.2, 6.2.0
+| align="center" | 6.2.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. Homepage: https://gmplib.org/ URL: https://gmplib.org/<br /><br /><br /></div>
-|-
-| align="center" | [https://www.google.ca/search?q=gmpich gmpich]
-| align="center" | -
-| align="center" | 2019.05
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: gcc and GFortran based compiler toolchain, including MPICH for MPI support. Homepage: (none)<br /><br /><br /></div>
 |-
 | align="center" | [https://gmsh.info/ gmsh]
 | align="center" | phys
-| align="center" | 3.0.6, 4.0.7, 4.7.0, 4.10.5, 4.11.1, 4.12.2
+| align="center" | 4.7.0, 4.10.5, 4.11.1, 4.12.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. Homepage: https://gmsh.info/ URL: https://gmsh.info/ Keyword:phys<br /><br /><br /></div>
 |-
 | align="center" | [https://www.generic-mapping-tools.org/ gmt]
 | align="center" | geo
-| align="center" | 5.4.2, 6.2.0, 6.5.0
+| align="center" | 6.5.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools. Homepage: https://www.generic-mapping-tools.org/ URL: https://www.generic-mapping-tools.org/ Keyword:geo<br /><br /><br /></div>
 |-
@@ Line 1,827: / Line 1,592: @@
 | align="center" | [http://gnuplot.sourceforge.net gnuplot]
 | align="center" | vis
-| align="center" | 5.2.5, 5.2.8, 5.4.2, 5.4.6, 5.4.8
+| align="center" | 5.2.8, 5.4.2, 5.4.6, 5.4.8
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Portable interactive, function plotting utility Homepage: http://gnuplot.sourceforge.net URL: http://gnuplot.sourceforge.net Keyword:vis<br /><br /><br /></div>
 |-
 | align="center" | [https://www.golang.org go]
 | align="center" | tools
-| align="center" | 1.10.3, 1.14.1, 1.14.4, 1.18.3, 1.21.3
+| align="center" | 1.14.1, 1.18.3, 1.21.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Go is an open source programming language that makes it easy to build simple, reliable, and efficient software. Homepage: https://www.golang.org URL: https://www.golang.org Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 1,847: / Line 1,612: @@
 | align="center" | [https://github.com/google/googletest googletest]
 | align="center" | tools
-| align="center" | 1.8.0, 1.10.0, 1.13.0, 1.14.0
+| align="center" | 1.10.0, 1.13.0, 1.14.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Google's framework for writing C++ tests on a variety of platforms Homepage: https://github.com/google/googletest URL: https://github.com/google/googletest Keyword:tools<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/data61/gossamer gossamer]
-| align="center" | bio
-| align="center" | 0.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Gossamer bioinformatics suite Homepage: https://github.com/data61/gossamer Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/jmrosinski/GPTL gptl]
-| align="center" | -
-| align="center" | 8.0.2
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: General Purpose Timing Library Homepage: https://github.com/jmrosinski/GPTL URL: https://github.com/jmrosinski/GPTL<br /><br /><br /></div>
 |-
 | align="center" | [http://freecode.com/projects/grace grace]
 | align="center" | vis
 | align="center" | 5.99.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. Homepage: http://freecode.com/projects/grace Keyword:vis<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. Homepage: http://freecode.com/projects/grace URL: http://freecode.com/projects/grace Keyword:vis<br /><br /><br /></div>
-|-
-| align="center" | [http://grackle.readthedocs.io grackle]
-| align="center" | phys
-| align="center" | 3.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Grackle is a chemistry and radiative cooling library for astrophysical simulations and models. Homepage: http://grackle.readthedocs.io Keyword:phys<br /><br /><br /></div>
 |-
 | align="center" | [https://graph-tool.skewed.de/ graph-tool]
@@ Line 1,877: / Line 1,627: @@
 | align="center" | [https://grass.osgeo.org grass]
 | align="center" | geo
-| align="center" | 7.4.0, 7.8.4, 8.2.1
+| align="center" | 7.8.4, 8.2.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization Homepage: https://grass.osgeo.org URL: https://grass.osgeo.org Keyword:geo<br /><br /><br /></div>
 |-
-| align="center" | [https://software.ecmwf.int/wiki/display/GRIB/Home grib_api]
+| align="center" | [https://www.gnu.org/software/groff groff]
-| align="center" | -
-| align="center" | 1.28.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The ECMWF GRIB API is an application program interface accessible from C, FORTRAN and Python programs developed for encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages. A useful set of command line tools is also provided to give quick access to GRIB messages. Homepage: https://software.ecmwf.int/wiki/display/GRIB/Home<br /><br /><br /></div>
-|-
-| align="center" | [https://www.gnu.org/software/groff groff]
 | align="center" | -
 | align="center" | 1.22.4
@@ Line 1,892: / Line 1,637: @@
 | align="center" | [http://www.gromacs.org gromacs]
 | align="center" | chem
-| align="center" | 2018.3, 2018.6, 2018.7, 2019.1, 2019.3, 2019.6, 2020.2, 2020.4, 2020.6, 2021.2, 2021.4, 2021.6, 2022.2, 2022.3, 2023, 2023.2, 2023.3, 2024.1
+| align="center" | 2020.4, 2020.6, 2021.2, 2021.4, 2021.6, 2022.2, 2022.3, 2023, 2023.2, 2023.3, 2024.1
 | Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a CPU only build, containing both MPI and threadMPI builds. Homepage: http://www.gromacs.org URL: http://www.gromacs.org Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 1,907: / Line 1,652: @@
 | align="center" | [http://www.gromacs.org gromacs-plumed]
 | align="center" | chem
-| align="center" | 2018.1, 2019.5, 2019.6, 2021.2, 2021.4, 2021.6, 2021.7, 2022.3, 2022.6
+| align="center" | 2019.6, 2021.2, 2021.4, 2021.6, 2021.7, 2022.3, 2022.6
 | Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics. This version contains the PLUMED patches in order to run metadynamics. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org URL: http://www.gromacs.org Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 1,913: / Line 1,658: @@
 | align="center" | chem
 | align="center" | 2020.5-RAMD-2.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics. This version has been modified to support RAMD, which is used to identify ligand exit routes from the buried binding pockets of receptors and investigate the mechanism of ligand dissociation. https://kbbox.h-its.org/toolbox/methods/molecular-simulation/random-acceleration-molecular-dynamics-ramd/ This is a GPU enabled build, containing both MPI and threadMPI binaries. Homepage: https://github.com/HITS-MCM/gromacs-ramd URL: https://github.com/HITS-MCM/gromacs-ramd Keyword:chem<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics. This version has been modified to support RAMD, which is used to identify ligand exit routes from the buried binding pockets of receptors and investigate the mechanism of ligand dissociation. https://kbbox.h-its.org/toolbox/methods/molecular-simulation/random-acceleration-molecular-dynamics-ramd/ This is a CPU only build, containing both MPI and threadMPI builds. Homepage: https://github.com/HITS-MCM/gromacs-ramd URL: https://github.com/HITS-MCM/gromacs-ramd Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://cbjh.gitlab.io/gromacs-swaxs-docs/ gromacs-swaxs]
 | align="center" | chem
 | align="center" | 2021.7-0.5.1
-| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Modified GROMACS for small-angle scattering calculations (SAXS/WAXS/SANS). This is a CPU only build, containing both MPI and threadMPI builds. - CC-Wiki: GROMACS Homepage: https://cbjh.gitlab.io/gromacs-swaxs-docs/ URL: https://cbjh.gitlab.io/gromacs-swaxs-docs/ Keyword:chem<br /><br /><br /></div>
+| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Modified GROMACS for small-angle scattering calculations (SAXS/WAXS/SANS). This is a GPU enabled build, containing both MPI and threadMPI builds. - CC-Wiki: GROMACS Homepage: https://cbjh.gitlab.io/gromacs-swaxs-docs/ URL: https://cbjh.gitlab.io/gromacs-swaxs-docs/ Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://www.gnu.org/software/gsl/ gsl]
 | align="center" | math
-| align="center" | 1.16, 2.2.1, 2.3, 2.4, 2.5, 2.6, 2.7
+| align="center" | 1.16, 2.6, 2.7
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. Homepage: https://www.gnu.org/software/gsl/ URL: https://www.gnu.org/software/gsl/ Keyword:math<br /><br /><br /></div>
 |-
@@ Line 1,929: / Line 1,674: @@
 | align="center" | 0.40.0, 0.41.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A single-file header-only version of ISO C++ Guidelines Support Library (GSL) for C++98, C++11, and later Homepage: https://github.com/gsl-lite/gsl-lite URL: https://github.com/gsl-lite/gsl-lite<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/google/googletest gtest]
-| align="center" | -
-| align="center" | 1.10.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Google's framework for writing C++ tests on a variety of platforms Homepage: https://github.com/google/googletest URL: https://github.com/google/googletest<br /><br /><br /></div>
-|-
-| align="center" | [https://www.gtk.org/ gtk+3]
-| align="center" | tools
-| align="center" | 3.20.9
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GTK+, or the GIMP Toolkit, is a multi-platform toolkit for creating graphical user interfaces. Offering a complete set of widgets, GTK+ is suitable for projects ranging from small one-off tools to complete application suites. Homepage: https://www.gtk.org/ Keyword:tools<br /><br /><br /></div>
-|-
-| align="center" | [http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html gtool]
-| align="center" | -
-| align="center" | 0.7.5
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. Homepage: http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html URL: http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html<br /><br /><br /></div>
 |-
 | align="center" | [http://gts.sourceforge.net/ gts]
 | align="center" | -
-| align="center" | 0.7.6, 20121130
+| align="center" | 20121130
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles. Homepage: http://gts.sourceforge.net/ URL: http://gts.sourceforge.net/<br /><br /><br /></div>
 |-
@@ Line 1,954: / Line 1,684: @@
 | align="center" | 3.4.1, 3.7.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The GUDHI library is a generic open source C++ library, with a Python interface, for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding. The library offers state-of-the-art data structures and algorithms to construct simplicial complexes and compute persistent homology. The library comes with data sets, demos, examples and test suites. Homepage: https://gudhi.inria.fr/ URL: https://gudhi.inria.fr/ Compatible modules: python/3.10, python/3.9, python/3.8<br /><br /><br /></div>
-|-
-| align="center" | [http://www.gnu.org/software/guile guile]
-| align="center" | tools
-| align="center" | 1.8.8
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system. Homepage: http://www.gnu.org/software/guile Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://www.gurobi.com gurobi]
 | align="center" | math
-| align="center" | 8.1.1, 9.0.1, 9.0.2, 9.0.3, 9.1.0, 9.1.2, 9.5.0, 9.5.2, 10.0.1, 10.0.2, 10.0.3, 11.0.0, 11.0.1
+| align="center" | 9.0.3, 9.1.0, 9.1.2, 9.5.0, 9.5.2, 10.0.1, 10.0.2, 10.0.3, 11.0.0, 11.0.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms. Homepage: https://www.gurobi.com URL: https://www.gurobi.com Keyword:math<br /><br /><br /></div>
 |-
@@ Line 1,982: / Line 1,707: @@
 | align="center" | [https://github.com/NanoComp/harminv harminv]
 | align="center" | math
-| align="center" | 1.4, 1.4.1
+| align="center" | 1.4.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids. Homepage: https://github.com/NanoComp/harminv URL: https://github.com/NanoComp/harminv Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [https://www.hdfgroup.org/products/hdf4/ hdf]
 | align="center" | io
-| align="center" | 4.2.12, 4.2.15, 4.2.16
+| align="center" | 4.2.15, 4.2.16
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. Homepage: https://www.hdfgroup.org/products/hdf4/ URL: https://www.hdfgroup.org/products/hdf4/ Keyword:io<br /><br /><br /></div>
 |-
@@ Line 2,002: / Line 1,727: @@
 | align="center" | [https://portal.hdfgroup.org/display/support hdf5]
 | align="center" | io
-| align="center" | 1.8.18, 1.8.20, 1.8.21, 1.8.22, 1.10.1, 1.10.3, 1.10.5, 1.10.6, 1.10.7, 1.12.1, 1.12.2, 1.14.2
+| align="center" | 1.8.22, 1.10.6, 1.10.7, 1.12.1, 1.12.2, 1.14.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. Homepage: https://portal.hdfgroup.org/display/support URL: https://portal.hdfgroup.org/display/support Compatible modules: python/3.10, python/3.11 Extensions: blosc2-2.2.9, cached-property-1.5.2, h5py-3.10.0, ndindex-1.7, numexpr-2.8.7, py-cpuinfo-9.0.0, tables-3.9.1 Keyword:io<br /><br /><br /></div>
 |-
 | align="center" | [https://portal.hdfgroup.org/display/support hdf5-mpi]
 | align="center" | io
-| align="center" | 1.8.18, 1.10.3, 1.10.6, 1.10.7, 1.12.1, 1.12.2, 1.14.2, 1.14.4
+| align="center" | 1.10.6, 1.10.7, 1.12.1, 1.12.2, 1.14.2, 1.14.4
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. Homepage: https://portal.hdfgroup.org/display/support URL: https://portal.hdfgroup.org/display/support Compatible modules: python/3.10, python/3.11, python/3.12 Extensions: blosc2-2.7.0, cached-property-1.5.2, h5py-3.11.0, ndindex-1.8, numexpr-2.10.1, py-cpuinfo-9.0.0, tables-3.9.2 Keyword:io<br /><br /><br /></div>
 |-
@@ Line 2,022: / Line 1,747: @@
 | align="center" | [https://heasarc.nasa.gov/lheasoft/ heasoft]
 | align="center" | phys
-| align="center" | 6.26.1, 6.32.1
+| align="center" | 6.32.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A Unified Release of the FTOOLS and XANADU Software Packages XANADU High-level, multi-mission tasks for X-ray astronomical spectral, timing, and imaging data analysis FTOOLS General and mission-specific tools to manipulate FITS files FITSIO Core library responsible for reading and writing FITS files (distributed with FTOOLS) fv General FITS file browser/editor/plotter with a graphical user interface (distributed with FTOOLS) XSTAR Tool for calculating the physical conditions and emission spectra of photoionized gases Homepage: https://heasarc.nasa.gov/lheasoft/ URL: https://heasarc.nasa.gov/lheasoft/ Extensions: Env-1.04, ExtUtils::MakeMaker-7.70, modules-0.04 Keyword:phys<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/soedinglab/hh-suite hh-suite]
 | align="center" | bio
-| align="center" | 3.0-beta.3, 3.3.0
+| align="center" | 3.3.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HH-suite is an open-source software package for sensitive protein sequence searching. It contains programs that can search for similar protein sequences in protein sequence databases. Homepage: https://github.com/soedinglab/hh-suite URL: https://github.com/soedinglab/hh-suite Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 2,042: / Line 1,767: @@
 | align="center" | [https://daehwankimlab.github.io/hisat2/ hisat2]
 | align="center" | bio
-| align="center" | 2.1.0, 2.2.0, 2.2.1
+| align="center" | 2.2.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). Homepage: https://daehwankimlab.github.io/hisat2/ URL: https://daehwankimlab.github.io/hisat2/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://hmmer.org/ hmmer]
 | align="center" | bio
-| align="center" | 3.1b2, 3.2.1, 3.3.2, 3.4
+| align="center" | 3.2.1, 3.3.2, 3.4
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST. Homepage: http://hmmer.org/ URL: http://hmmer.org/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 2,072: / Line 1,797: @@
 | align="center" | [https://www.netlib.org/benchmark/hpl/ hpl]
 | align="center" | tools
-| align="center" | 2.2, 2.3
+| align="center" | 2.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark. Homepage: https://www.netlib.org/benchmark/hpl/ URL: https://www.netlib.org/benchmark/hpl/ Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 2,087: / Line 1,812: @@
 | align="center" | [https://veg.github.io/hyphy-site/ hyphy]
 | align="center" | bio
-| align="center" | 2.3.14, 2.5.26, 2.5.49
+| align="center" | 2.5.26, 2.5.49
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning Homepage: https://veg.github.io/hyphy-site/ URL: https://veg.github.io/hyphy-site/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods hypre]
 | align="center" | math
-| align="center" | 2.15.1, 2.20.0
+| align="center" | 2.20.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences. Homepage: https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods URL: https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods Keyword:math<br /><br /><br /></div>
-|-
-| align="center" | [http://www.ichthyop.org/ ichthyop]
-| align="center" | -
-| align="center" | 3.3.3
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Ichthyop is a free Java tool designed to study the effects of physical and biological factors on ichthyoplankton dynamics. It incorporates the most important processes involved in fish early life: spawning, movement, growth, mortality and recruitment. The tool uses as input time series of velocity, temperature and salinity fields archived from ROMS, MARS, NEMO or SYMPHONIE oceanic models (either files or OpenDAP). Homepage: http://www.ichthyop.org/<br /><br /><br /></div>
 |-
 | align="center" | [http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/ idba-ud]
 | align="center" | -
 | align="center" | 1.1.3
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions. Homepage: http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions. Homepage: http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/ URL: http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/<br /><br /><br /></div>
 |-
 | align="center" | [https://www.ncbi.nlm.nih.gov/igblast/intro.html igblast]
 | align="center" | bio
-| align="center" | 1.8.0, 1.9.0, 1.16.0, 1.17.0, 1.18.0
+| align="center" | 1.17.0, 1.18.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin variable domain sequences (IgBLAST has recently been extended to perform analysis for T cell receptor (TR) sequences). It uses BLAST search algorithm. Homepage: https://www.ncbi.nlm.nih.gov/igblast/intro.html URL: https://www.ncbi.nlm.nih.gov/igblast/intro.html Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 2,117: / Line 1,837: @@
 | align="center" | [https://igraph.org igraph]
 | align="center" | math
-| align="center" | 0.7.1, 0.8.2, 0.9.10, 0.10.2, 0.10.7
+| align="center" | 0.8.2, 0.9.10, 0.10.2, 0.10.7
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++. Homepage: https://igraph.org URL: https://igraph.org Compatible modules: python/3.10, python/3.11 Extensions: python-igraph-0.11.2 Keyword:math<br /><br /><br /></div>
 |-
@@ Line 2,134: / Line 1,854: @@
 | align="center" | 1.12, 20210120
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IMa3 is the newest in the IM sequence of programs. It can be used to solve a fundamental problem in evolutionary genetics, which is to jointly consider phylogenetic history and pouplation genetic history, including gene exchange. IMa3 can be used to estimate the rooted phylogenetic tree for multiple populations, and does so while integrating over all possible Isolation-with-Migration models. For a given phylogenetic tree IMa3 addresses the same model as IMa2. Like IMa2-p, IMa3 can run on multiple processors. Homepage: https://github.com/jodyhey/IMa3 URL: https://github.com/jodyhey/IMa3<br /><br /><br /></div>
-|-
-| align="center" | [http://www.imagemagick.org/ imagemagick]
-| align="center" | -
-| align="center" | 7.0.8-53
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ImageMagick is a software suite to create, edit, compose, or convert bitmap images Homepage: http://www.imagemagick.org/<br /><br /><br /></div>
 |-
 | align="center" | [https://software.intel.com/en-us/articles/intel-mpi-benchmarks imb]
@@ Line 2,147: / Line 1,862: @@
 | align="center" | [https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html imkl]
 | align="center" | math
-| align="center" | 11.1.4.214, 11.3.4.258, 2017.1.132, 2017.4.239, 2018.1.163, 2018.3.222, 2019.2.187, 2019.3.199, 2020.1.217, 2021.2.0, 2021.4.0, 2022.1.0, 2023.2.0, 2024.1.0
+| align="center" | 2020.1.217, 2021.2.0, 2021.4.0, 2022.1.0, 2023.2.0, 2024.1.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel oneAPI Math Kernel Library Homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html URL: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html Keyword:math<br /><br /><br /></div>
-|-
-| align="center" | [http://software.intel.com/en-us/intel-mpi-library/ impi]
-| align="center" | mpi
-| align="center" | 2018.3.222
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel MPI Library, compatible with MPICH ABI Homepage: http://software.intel.com/en-us/intel-mpi-library/<br /><br /><br /></div>
 |-
 | align="center" | [http://mathgen.stats.ox.ac.uk/impute/impute_v2.html impute2]
 | align="center" | bio
 | align="center" | 2.3.2
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009 - Homepage: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009 Homepage: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html URL: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://jmarchini.org/software/#impute-5 impute5]
@@ Line 2,167: / Line 1,877: @@
 | align="center" | [http://eddylab.org/infernal/ infernal]
 | align="center" | bio
-| align="center" | 1.1.2, 1.1.3, 1.1.4, 1.1.5
+| align="center" | 1.1.3, 1.1.4, 1.1.5
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. Homepage: http://eddylab.org/infernal/ URL: http://eddylab.org/infernal/ Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://software.intel.com/en-us/intel-inspector-xe inspector]
-| align="center" | tools
-| align="center" | 2018.3
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications Homepage: http://software.intel.com/en-us/intel-inspector-xe Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html intel]
 | align="center" | tools
-| align="center" | 2014.6, 2016.4, 2017.1, 2017.5, 2018.3, 2019.3, 2020.1.217, 2021.2.0, 2022.1.0, 2023.2.1
+| align="center" | 2020.1.217, 2021.2.0, 2022.1.0, 2023.2.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel C, C++ and Fortran compilers (classic and oneAPI) Homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html URL: https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 2,187: / Line 1,892: @@
 | align="center" | [https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html intelmpi]
 | align="center" | mpi
-| align="center" | 2018.3.222, 2019.3.199, 2019.7.217, 2021.2.0, 2021.9.0
+| align="center" | 2019.7.217, 2021.2.0, 2021.9.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel MPI Library, compatible with MPICH ABI Homepage: https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html URL: https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html<br /><br /><br /></div>
 |-
@@ Line 2,197: / Line 1,902: @@
 | align="center" | [http://www.ebi.ac.uk/interpro/ interproscan]
 | align="center" | bio
-| align="center" | 5.23-62.0, 5.40-77.0, 5.50-84.0, 5.52-86.0, 5.53-87.0, 5.55-88.0, 5.56-89.0, 5.63-95.0, 5.64-96.0
+| align="center" | 5.52-86.0, 5.55-88.0, 5.56-89.0, 5.53-87.0, 5.64-96.0, 5.63-95.0, 5.50-84.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. Homepage: http://www.ebi.ac.uk/interpro/ URL: http://www.ebi.ac.uk/interpro/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 2,217: / Line 1,922: @@
 | align="center" | [https://projects.coin-or.org/Ipopt ipopt]
 | align="center" | -
-| align="center" | 3.12.13, 3.14.11, 3.14.14
+| align="center" | 3.14.11, 3.14.14
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IPOPT (Interior Point Optimizer, pronounced Eye-Pea-Opt) is an open source software package for large-scale nonlinear optimization. Homepage: https://projects.coin-or.org/Ipopt URL: https://projects.coin-or.org/Ipopt<br /><br /><br /></div>
 |-
 | align="center" | [https://software.intel.com/en-us/articles/intel-ipp/ ipp]
 | align="center" | tools
-| align="center" | 9.0.4, 2017.1.132, 2020.1.217
+| align="center" | 2020.1.217
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms. Homepage: https://software.intel.com/en-us/articles/intel-ipp/ URL: https://software.intel.com/en-us/articles/intel-ipp/ Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 2,232: / Line 1,937: @@
 | align="center" | [https://ipython.org/ ipython-kernel]
 | align="center" | -
-| align="center" | 2.7, 3.5, 3.6, 3.7, 3.8, 3.9, 3.10, 3.11, 3.12
+| align="center" | 2.7, 3.6, 3.7, 3.8, 3.9, 3.10, 3.11, 3.12
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IPython kernelspec for Python 3.12 Homepage: https://ipython.org/ URL: https://ipython.org/<br /><br /><br /></div>
 |-
 | align="center" | [http://www.iqtree.org/ iq-tree]
 | align="center" | bio
-| align="center" | 1.5.5, 1.6.12, 2.0-rc2, 2.0.7, 2.1.2, 2.2.1, 2.2.2.7
+| align="center" | 1.6.12, 2.0.7, 2.1.2, 2.2.1, 2.2.2.7
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Efficient phylogenomic software by maximum likelihood Homepage: http://www.iqtree.org/ URL: http://www.iqtree.org/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 2,247: / Line 1,952: @@
 | align="center" | [https://github.com/williamritchie/IRFinder/ irfinder]
 | align="center" | -
-| align="center" | 1.2.6, 1.3.1
+| align="center" | 1.3.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Basic STAR (Spliced Transcripts Alignment to a Reference) STAR workflow consists of 2 steps: Generating genoms indexes files and mapping reads to the genomes. Homepage: https://github.com/williamritchie/IRFinder/ URL: https://github.com/williamritchie/IRFinder/ Extensions: Data::Dumper-2.173<br /><br /><br /></div>
 |-
@@ Line 2,262: / Line 1,967: @@
 | align="center" | [https://software.intel.com/en-us/intel-trace-analyzer/ itac]
 | align="center" | tools
-| align="center" | 2018.3.022, 2021.5.0
+| align="center" | 2021.5.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. Homepage: https://software.intel.com/en-us/intel-trace-analyzer/ URL: https://software.intel.com/en-us/intel-trace-analyzer/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://itk.org itk]
 | align="center" | vis
-| align="center" | 4.13.1, 4.13.3, 5.0.1, 5.1.2, 5.2.1, 5.3.0
+| align="center" | 4.13.3, 5.0.1, 5.1.2, 5.2.1, 5.3.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. Homepage: https://itk.org URL: https://itk.org Compatible modules: python/3.11, python/3.10 Keyword:vis<br /><br /><br /></div>
 |-
@@ Line 2,282: / Line 1,987: @@
 | align="center" | [https://www.ece.uvic.ca/~frodo/jasper/ jasper]
 | align="center" | vis
-| align="center" | 1.900.1, 2.0.16, 4.0.0
+| align="center" | 2.0.16, 4.0.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard. Homepage: https://www.ece.uvic.ca/~frodo/jasper/ URL: https://www.ece.uvic.ca/~frodo/jasper/ Keyword:vis<br /><br /><br /></div>
 |-
 | align="center" | [http://openjdk.java.net java]
 | align="center" | tools
-| align="center" | 1.7.0_80, 1.8.0_121, 1.8.0_192, 1.8.0_292, 11.0.16_8, 11.0.22, 13.0.1, 13.0.2, 14.0.2, 17.0.2, 17.0.6, 21.0.1
+| align="center" | 1.8.0_192, 1.8.0_292, 11.0.16_8, 11.0.22, 13.0.2, 14.0.2, 17.0.2, 17.0.6, 21.0.1
 | Documentation: [[Java]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. Homepage: http://openjdk.java.net URL: http://openjdk.java.net Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 2,297: / Line 2,002: @@
 | align="center" | [http://jdftx.org/index.html jdftx]
 | align="center" | chem
-| align="center" | 1.4.2, 1.7.0
+| align="center" | 1.7.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: JDFTx is a plane-wave density-functional theory (DFT) code designed to be as easy to develop with as it is easy to use. It is distributed under the GPL license (version 3 or higher) and publications resulting from its use must cite: R. Sundararaman, K. Letchworth-Weaver, K.A. Schwarz, D. Gunceler, Y. Ozhabes and T.A. Arias, 'JDFTx: software for joint density-functional theory Homepage: http://jdftx.org/index.html URL: http://jdftx.org/index.html Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [http://www.genome.umd.edu/jellyfish.html jellyfish]
 | align="center" | bio
-| align="center" | 2.2.6, 2.2.10, 2.3.0
+| align="center" | 2.3.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. Homepage: http://www.genome.umd.edu/jellyfish.html URL: http://www.genome.umd.edu/jellyfish.html Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 2,322: / Line 2,027: @@
 | align="center" | [https://julialang.org julia]
 | align="center" | tools
-| align="center" | 1.0.2, 1.1.0, 1.1.1, 1.2.0, 1.3.0, 1.4.0, 1.4.1, 1.5.2, 1.6.0, 1.6.1, 1.7.0, 1.8.1, 1.8.5, 1.9.1, 1.9.3, 1.10.0
+| align="center" | 1.4.1, 1.5.2, 1.6.0, 1.6.1, 1.7.0, 1.8.1, 1.8.5, 1.9.1, 1.9.3, 1.10.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Julia is a high-level, high-performance dynamic programming language for numerical computing Homepage: https://julialang.org URL: https://julialang.org Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 2,347: / Line 2,052: @@
 | align="center" | [https://pachterlab.github.io/kallisto/ kallisto]
 | align="center" | bio
-| align="center" | 0.44.0, 0.45.0, 0.46.0, 0.46.1
+| align="center" | 0.46.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. Homepage: https://pachterlab.github.io/kallisto/ URL: https://pachterlab.github.io/kallisto/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://genome.cse.ucsc.edu/ kentutils]
 | align="center" | bio
-| align="center" | 401, 20180716
+| align="center" | 401
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Kent utilities: collection of tools used by the UCSC genome browser. Homepage: http://genome.cse.ucsc.edu/ Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Kent utilities: collection of tools used by the UCSC genome browser. Homepage: http://genome.cse.ucsc.edu/ URL: http://genome.cse.ucsc.edu/ Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [https://openkim.org/ kim]
-| align="center" | chem
-| align="center" | 1.8.2, 1.9.7, 2.1.3
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenKIM is an online suite of open source tools for molecular simulation of materials. These tools help to make molecular simulation more accessible and more reliable. Within OpenKIM, you will find an online resource for standardized testing and long-term warehousing of interatomic models and data, and an application programming interface (API) standard for coupling atomistic simulation codes and interatomic potential subroutines. Homepage: https://openkim.org/ URL: https://openkim.org/ Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://openkim.org/ kim-api]
@@ Line 2,374: / Line 2,074: @@
 | align="center" | 1.7051
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: KmerGenie estimates the best k-mer length for genome de novo assembly. Homepage: http://kmergenie.bx.psu.edu/ URL: http://kmergenie.bx.psu.edu/<br /><br /><br /></div>
-|-
-| align="center" | [https://www.knime.com/ knime]
-| align="center" | -
-| align="center" | 4.1.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: KNIME Analytics Platform is the open source software for creating data science applications and services. KNIME stands for KoNstanz Information MinEr. Homepage: https://www.knime.com/ URL: https://www.knime.com/<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/kokkos/ kokkos]
-| align="center" | tools
-| align="center" | 2.7.24
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Kokkos implements a programming model in C++ for writing performance portable applications targeting all major HPC platforms. For that purpose it provides abstractions for both parallel execution of code and data management. Kokkos is designed to target complex node architectures with N-level memory hierarchies and multiple types of execution resources. It currently can use OpenMP, Pthreads and CUDA as backend programming models. Homepage: https://github.com/kokkos/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/eclarke/komplexity komplexity]
@@ Line 2,392: / Line 2,082: @@
 | align="center" | [https://ccb.jhu.edu/software/kraken/ kraken]
 | align="center" | bio
-| align="center" | 1.1, 1.1.1
+| align="center" | 1.1.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Homepage: https://ccb.jhu.edu/software/kraken/ URL: https://ccb.jhu.edu/software/kraken/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/DerrickWood/kraken2/wiki kraken2]
 | align="center" | bio
-| align="center" | 2.0.7-beta, 2.0.8-beta, 2.0.9-beta, 2.1.1, 2.1.2, 2.1.3
+| align="center" | 2.0.9-beta, 2.1.1, 2.1.2, 2.1.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Homepage: https://github.com/DerrickWood/kraken2/wiki URL: https://github.com/DerrickWood/kraken2/wiki Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 2,412: / Line 2,102: @@
 | align="center" | [https://www.lammps.org lammps-omp]
 | align="center" | chem
-| align="center" | 20190807, 20201029, 20210929, 20220623, 20230802
+| align="center" | 20201029, 20210929, 20220623, 20230802
 | Documentation: [[LAMMPS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. Homepage: https://www.lammps.org URL: https://www.lammps.org Compatible modules: python/3.11, python/3.10 Keyword:chem<br /><br /><br /></div>
-|-
-| align="center" | [http://lammps.sandia.gov/ lammps-user-intel]
-| align="center" | chem
-| align="center" | 20180822
-| Documentation: [[LAMMPS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics simulation. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. It can be coupled to various programs. The following packages are not included within this version: -GPU, -KOKKOS, -MANYBODY, -MSCG, -QEQ, -USER-ATC, -USER-QUIP Homepage: http://lammps.sandia.gov/ Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [http://last.cbrc.jp/ last]
 | align="center" | bio
-| align="center" | 959, 1145
+| align="center" | 1145
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LAST finds similar regions between sequences. Homepage: http://last.cbrc.jp/ URL: http://last.cbrc.jp/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 2,433: / Line 2,118: @@
 | align="center" | chem
 | align="center" | 1.2.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Open source density functional tight binding molecular dynamics. Homepage: https://github.com/lanl/LATTE Keyword:chem<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Open source density functional tight binding molecular dynamics. Homepage: https://github.com/lanl/LATTE URL: https://github.com/lanl/LATTE Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://wiki.dlang.org/LDC ldc]
@@ Line 2,452: / Line 2,137: @@
 | align="center" | [https://github.com/google/leveldb leveldb]
 | align="center" | tools
-| align="center" | 1.18, 1.20, 1.22
+| align="center" | 1.22
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values. Homepage: https://github.com/google/leveldb URL: https://github.com/google/leveldb Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 2,487: / Line 2,172: @@
 | align="center" | [https://jugit.fz-juelich.de/mlz/libcerf libcerf]
 | align="center" | math
-| align="center" | 1.5, 1.13, 1.17, 2.1, 2.4
+| align="center" | 1.13, 1.17, 2.1, 2.4
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions. Homepage: https://jugit.fz-juelich.de/mlz/libcerf URL: https://jugit.fz-juelich.de/mlz/libcerf Keyword:math<br /><br /><br /></div>
 |-
@@ Line 2,494: / Line 2,179: @@
 | align="center" | 1.0.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Climate Data Management System Library. Homepage: https://github.com/CDAT/libcf/ URL: https://github.com/CDAT/libcf/<br /><br /><br /></div>
-|-
-| align="center" | [http://www.hyperrealm.com/libconfig/ libconfig]
-| align="center" | tools
-| align="center" | 1.7.2
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Libconfig is a simple library for processing structured configuration files Homepage: http://www.hyperrealm.com/libconfig/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/NanoComp/libctl libctl]
 | align="center" | tools
-| align="center" | 3.2.2, 4.5.0
+| align="center" | 4.5.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: libctl is a free Guile-based library implementing flexible control files for scientific simulations. Homepage: https://github.com/NanoComp/libctl URL: https://github.com/NanoComp/libctl Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 2,537: / Line 2,217: @@
 | align="center" | [https://libgd.github.io libgd]
 | align="center" | vis
-| align="center" | 2.2.5, 2.3.0, 2.3.3
+| align="center" | 2.3.0, 2.3.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GD is an open source code library for the dynamic creation of images by programmers. Homepage: https://libgd.github.io URL: https://libgd.github.io Keyword:vis<br /><br /><br /></div>
 |-
@@ Line 2,568: / Line 2,248: @@
 | align="center" | bio
 | align="center" | 0.7
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream Homepage: http://hannonlab.cshl.edu/fastx_toolkit/ Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream Homepage: http://hannonlab.cshl.edu/fastx_toolkit/ URL: http://hannonlab.cshl.edu/fastx_toolkit/ Keyword:bio<br /><br /><br /></div>
 |-
-| align="center" | [http://libharu.org/ libharu]
+| align="center" | [https://github.com/libharu/libharu/ libharu]
 | align="center" | -
 | align="center" | 2.3.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: libHaru is a free, cross platform, open source library for generating PDF files. Homepage: http://libharu.org/ URL: http://libharu.org/<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: libHaru is a free, cross platform, open source library for generating PDF files. Homepage: https://github.com/libharu/libharu/ URL: https://github.com/libharu/libharu/<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/evaleev/libint libint]
 | align="center" | chem
-| align="center" | 1.1.6, 2.0.3, 2.2.0, 2.4.2, 2.6.0
+| align="center" | 1.1.6, 2.0.3, 2.4.2, 2.6.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. Homepage: https://github.com/evaleev/libint URL: https://github.com/evaleev/libint Keyword:chem<br /><br /><br /></div>
-|-
-| align="center" | [http://www.gnu.org/software/libmatheval/ libmatheval]
-| align="center" | math
-| align="center" | 1.1.11
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. Homepage: http://www.gnu.org/software/libmatheval/ Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/gt1/libmaus2 libmaus2]
@@ Line 2,592: / Line 2,267: @@
 | align="center" | [https://github.com/libMesh/libmesh libmesh]
 | align="center" | math
-| align="center" | 1.2.1, 1.7.1
+| align="center" | 1.7.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The libMesh library provides a framework for the numerical simulation of partial differential equations using arbitrary unstructured discretizations on serial and parallel platforms. A major goal of the library is to provide support for adaptive mesh refinement (AMR) computations in parallel while allowing a research scientist to focus on the physics they are modeling. Homepage: https://github.com/libMesh/libmesh URL: https://github.com/libMesh/libmesh Keyword:math<br /><br /><br /></div>
 |-
-| align="center" | [https://bazaar.launchpad.net/~libomm-team/libomm/trunk/ libomm]
+| align="center" | [https://gitlab.com/siesta-project/libraries/libpsml libpsml]
 | align="center" | -
-| align="center" | 2015-06-05
+| align="center" | 1.1.8, 1.1.12
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: libOMM solves the Kohn-Sham equation as a generalized eigenvalue problem for a fixed Hamiltonian. It implements the orbital minimization method (OMM), which works within a density matrix formalism. Homepage: https://bazaar.launchpad.net/~libomm-team/libomm/trunk/<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/mfranberg/libplinkio libplinkio]
-| align="center" | bio
-| align="center" | 0.9.5
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A small C and Python library for reading PLINK genotype files. Homepage: https://github.com/mfranberg/libplinkio Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [https://gitlab.com/siesta-project/libraries/libpsml libpsml]
-| align="center" | -
-| align="center" | 1.1.8, 1.1.12
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A library to handle pseudopotentials in PSML format Homepage: https://gitlab.com/siesta-project/libraries/libpsml URL: https://gitlab.com/siesta-project/libraries/libpsml<br /><br /><br /></div>
-|-
-| align="center" | [http://libqglviewer.com/ libqglviewer]
-| align="center" | -
-| align="center" | 2.7.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers. Homepage: http://libqglviewer.com/ URL: http://libqglviewer.com/<br /><br /><br /></div>
 |-
 | align="center" | [https://www.libraw.org/ libraw]
@@ Line 2,634: / Line 2,294: @@
 | align="center" | 1.1.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The RT Topology Library exposes an API to create and manage standard (ISO 13249 aka SQL/MM) topologies Homepage: https://git.osgeo.org/gitea/rttopo/librttopo URL: https://git.osgeo.org/gitea/rttopo/librttopo<br /><br /><br /></div>
-|-
-| align="center" | [https://doc.libsodium.org/ libsodium]
-| align="center" | -
-| align="center" | 1.0.18
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. Homepage: https://doc.libsodium.org/ URL: https://doc.libsodium.org/<br /><br /><br /></div>
 |-
 | align="center" | [https://libspatialindex.org libspatialindex]
@@ Line 2,664: / Line 2,319: @@
 | align="center" | 20190330
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Useful set of classes for creating statistical genetic programs. Homepage: https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen URL: https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen<br /><br /><br /></div>
-|-
-| align="center" | [https://www.csie.ntu.edu.tw/~cjlin/libsvm/ libsvm]
-| align="center" | -
-| align="center" | 3.24
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). Homepage: https://www.csie.ntu.edu.tw/~cjlin/libsvm/ URL: https://www.csie.ntu.edu.tw/~cjlin/libsvm/<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/nbigaouette/libtricubic libtricubic]
-| align="center" | math
-| align="center" | 1.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Library implementing tricubic interpolation. Homepage: https://github.com/nbigaouette/libtricubic Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/axboe/liburing liburing]
@@ Line 2,682: / Line 2,327: @@
 | align="center" | [https://libxc.gitlab.io libxc]
 | align="center" | chem
-| align="center" | 2.2.2, 3.0.0, 3.0.1, 4.2.1, 4.2.3, 4.3.4, 5.0.0, 5.1.3, 5.2.3, 6.2.2
+| align="center" | 2.2.2, 3.0.0, 3.0.1, 4.3.4, 5.0.0, 5.1.3, 5.2.3, 6.2.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. Homepage: https://libxc.gitlab.io URL: https://libxc.gitlab.io Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 2,692: / Line 2,337: @@
 | align="center" | [https://github.com/hfp/libxsmm libxsmm]
 | align="center" | math
-| align="center" | 1.8.2, 1.16.1
+| align="center" | 1.16.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86). Homepage: https://github.com/hfp/libxsmm URL: https://github.com/hfp/libxsmm Keyword:math<br /><br /><br /></div>
 |-
@@ Line 2,701: / Line 2,346: @@
 |-
 | align="center" | [https://github.com/limix/liknorm liknorm]
-| align="center" | -
+| align="center" | tools
 | align="center" | 1.5.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C library for computing moments of the product of an exponential-family likelihood with a Normal distribution. Homepage: https://github.com/limix/liknorm URL: https://github.com/limix/liknorm<br /><br /><br /></div>
@@ Line 2,714: / Line 2,359: @@
 | align="center" | 1.8.6, 2.0.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LINKS is a scalable genomics application for scaffolding or re-scaffolding genome assembly drafts with long reads, such as those produced by Oxford Nanopore Technologies Ltd and Pacific Biosciences. It provides a generic alignment-free framework for scaffolding and can work on any sequences. It is versatile and supports not only long sequences as a source of long-range information, but also MPET pairs and linked-reads, such as those from the 10X Genomics GemCode and Chromium platform, via ARCS (http://www.bcgsc.ca/platform/bioinfo/software/arcs). Fill gaps in LINKS-derived scaffolds using Sealer (http://www.bcgsc.ca/platform/bioinfo/software/sealer). Homepage: http://www.bcgsc.ca/platform/bioinfo/software/links URL: http://www.bcgsc.ca/platform/bioinfo/software/links Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://www.netlib.org/misc/lis/ lis]
-| align="center" | math
-| align="center" | 2.0.10
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Lis, a Library of Iterative Solvers for linear systems, is a parallel library for solving linear equations and eigenvalue problems that arise in the numerical solution of partial differential equations using iterative methods. The installation of Lis requires a C compiler. The Fortran interface requires a Fortran compiler, and the algebraic multigrid preconditioner requires a Fortran 90 compiler. For parallel computing environments, an OpenMP or MPI-1 library is used. Both the Harwell-Boeing and Matrix Market formats are supported to import and export user data. Homepage: http://www.netlib.org/misc/lis/ Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [http://www.littlecms.com/ littlecms]
@@ Line 2,732: / Line 2,372: @@
 | align="center" | [https://llvm.org/ llvm]
 | align="center" | tools
-| align="center" | 6.0.1, 7.0.0, 8.0.1, 9.0.1, 13.0.1, 14.0.3, 16.0.6
+| align="center" | 8.0.1, 9.0.1, 13.0.1, 14.0.3, 16.0.6
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. Homepage: https://llvm.org/ URL: https://llvm.org/ Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 2,739: / Line 2,379: @@
 | align="center" | 0.9.24, 0.9.31
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases. Homepage: https://symas.com/lmdb URL: https://symas.com/lmdb<br /><br /><br /></div>
-|-
-| align="center" | [http://www.bioinf.uni-freiburg.de/Software/LocARNA/ locarna]
-| align="center" | bio
-| align="center" | 1.9.2.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LocARNA is a collection of alignment tools for the structural analysis of RNA. Given a set of RNA sequences, LocARNA simultaneously aligns and predicts common structures for your RNAs. In this way, LocARNA performs Sankoff-like alignment and is in particular suited for analyzing sets of related RNAs without known common structure. Homepage: http://www.bioinf.uni-freiburg.de/Software/LocARNA/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://sourceforge.net/projects/lpsolve/ lpsolve]
 | align="center" | math
 | align="center" | 5.5.2.5
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Mixed Integer Linear Programming (MILP) solver Homepage: https://sourceforge.net/projects/lpsolve/ Keyword:math<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Mixed Integer Linear Programming (MILP) solver Homepage: https://sourceforge.net/projects/lpsolve/ URL: https://sourceforge.net/projects/lpsolve/ Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [http://www.lstc.com/products/ls-opt ls-opt]
 | align="center" | phys
-| align="center" | 5.2.1, 7.0.0
+| align="center" | 7.0.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LS-OPT is a standalone Design Optimization and Probabilistic Analysis package with an interface to LS-DYNA. Homepage: http://www.lstc.com/products/ls-opt URL: http://www.lstc.com/products/ls-opt Keyword:phys<br /><br /><br /></div>
 |-
 | align="center" | [http://lstc.com/products/ls-prepost ls-prepost]
 | align="center" | -
-| align="center" | 4.7.8, 4.7.13, 4.8.11, 4.9.9
+| align="center" | 4.8.11, 4.9.9
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LS-PrePost is an advanced pre and post-processor that is delivered free with LS-DYNA. Homepage: http://lstc.com/products/ls-prepost URL: http://lstc.com/products/ls-prepost<br /><br /><br /></div>
 |-
@@ Line 2,773: / Line 2,408: @@
 | align="center" | bio
 | align="center" | 0.2.13
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A probabilistic framework for structural variant discovery. Homepage: https://github.com/arq5x/lumpy-sv Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A probabilistic framework for structural variant discovery. Homepage: https://github.com/arq5x/lumpy-sv URL: https://github.com/arq5x/lumpy-sv Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/Macaulay2/M2 m2]
@@ Line 2,779: / Line 2,414: @@
 | align="center" | 1.19.1, 1.21
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Macaulay2 is a system for computing in commutative algebra, algebraic geometry and related fields. The system was originally written by Dan Grayson and Mike Stillman. David Eisenbud joined the project a number of years ago, and many users are writing packages for the system, and some are contributing source code. Homepage: https://github.com/Macaulay2/M2 URL: https://github.com/Macaulay2/M2<br /><br /><br /></div>
-|-
-| align="center" | [http://csg.sph.umich.edu/abecasis/MACH/ mach]
-| align="center" | bio
-| align="center" | 1.0.18
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MACH 1.0 is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals. - Homepage: http://csg.sph.umich.edu/abecasis/MACH/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/schrodinger/maeparser maeparser]
@@ Line 2,797: / Line 2,427: @@
 | align="center" | [https://mafft.cbrc.jp/alignment/software/source.html mafft]
 | align="center" | bio
-| align="center" | 7.310, 7.397, 7.471
+| align="center" | 7.471
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of &lt;200 sequences), FFT-NS-2 (fast; for alignment of &lt;30,000 sequences), etc. Homepage: https://mafft.cbrc.jp/alignment/software/source.html URL: https://mafft.cbrc.jp/alignment/software/source.html Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 2,807: / Line 2,437: @@
 | align="center" | [https://icl.cs.utk.edu/magma/ magma]
 | align="center" | math
-| align="center" | 2.4.0, 2.5.0, 2.5.4, 2.6.1, 2.7.1, 2.7.2
+| align="center" | 2.5.4, 2.6.1, 2.7.1, 2.7.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems. Homepage: https://icl.cs.utk.edu/magma/ URL: https://icl.cs.utk.edu/magma/ Keyword:math<br /><br /><br /></div>
 |-
@@ Line 2,814: / Line 2,444: @@
 | align="center" | 1.10
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis. Homepage: https://ctg.cncr.nl/software/magma URL: https://ctg.cncr.nl/software/magma<br /><br /><br /></div>
-|-
-| align="center" | [http://www.gnu.org/software/make/make.html make]
-| align="center" | tools
-| align="center" | 3.82
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: make-3.82: GNU version of make utility Homepage: http://www.gnu.org/software/make/make.html Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://www.gnu.org/software/texinfo/ makeinfo]
@@ Line 2,832: / Line 2,457: @@
 | align="center" | [https://github.com/Illumina/manta manta]
 | align="center" | bio
-| align="center" | 1.2.2, 1.6.0
+| align="center" | 1.6.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow. Homepage: https://github.com/Illumina/manta URL: https://github.com/Illumina/manta Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 2,842: / Line 2,467: @@
 | align="center" | [https://docs.computecanada.ca/wiki/Database_servers. mariadb]
 | align="center" | tools
-| align="center" | 10.1.21, 10.4.11, 10.4.13, 10.6.12, 11.5.0
+| align="center" | 10.4.13, 10.6.12, 11.5.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MariaDB An enhanced, drop-in replacement for MySQL For more information please take a look at https://docs.computecanada.ca/wiki/Database_servers. Homepage: https://mariadb.org/ URL: https://mariadb.org/ Compatible modules: Extensions: DBD::mysql-5.004, Devel::CheckLib-1.16, IO::CaptureOutput-1.1105, mysql-connector-python-8.2.0, PyMySQL-1.1.0 Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 2,849: / Line 2,474: @@
 | align="center" | 3.1.7, 3.3.7
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases. Homepage: https://downloads.mariadb.org/connector-c/ URL: https://downloads.mariadb.org/connector-c/<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/schloi/MARVEL marvel]
-| align="center" | bio
-| align="center" | 1.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads. Homepage: https://github.com/schloi/MARVEL Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://mash.readthedocs.org mash]
@@ Line 2,862: / Line 2,482: @@
 | align="center" | [http://www.genome.umd.edu/masurca.html masurca]
 | align="center" | bio
-| align="center" | 3.2.8, 3.3.0, 3.4.1, 4.0.1, 4.0.3, 4.1.0
+| align="center" | 3.4.1, 4.0.1, 4.0.3, 4.1.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore). Homepage: http://www.genome.umd.edu/masurca.html URL: http://www.genome.umd.edu/masurca.html Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://sourceforge.net/projects/matio/ matio]
 | align="center" | io
-| align="center" | 1.5.2, 1.5.19, 1.5.26
+| align="center" | 1.5.19, 1.5.26
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: matio is an C library for reading and writing Matlab MAT files. Homepage: https://sourceforge.net/projects/matio/ URL: https://sourceforge.net/projects/matio/ Keyword:io<br /><br /><br /></div>
 |-
 | align="center" | [http://www.mathworks.com/products/matlab matlab]
 | align="center" | tools
-| align="center" | 2014a, 2016b, 2017a, 2018a, 2018b, 2019a, 2019b, 2020a, 2020b.4, 2020b.6, 2021a.1, 2021a.5, 2021b.3, 2022a, 2022b.2, 2023a.3, 2023b.2
+| align="center" | 2020a, 2020b, 2020b.4, 2020b.6, 2021a.1, 2021a.5, 2021b.3, 2022a, 2022b.2, 2023a.3, 2023b.2
 | Documentation: [[MATLAB]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. Homepage: http://www.mathworks.com/products/matlab URL: http://www.mathworks.com/products/matlab Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://maven.apache.org/index.html maven]
 | align="center" | tools
-| align="center" | 3.5.0, 3.6.3, 3.9.6
+| align="center" | 3.6.3, 3.9.6
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. Homepage: https://maven.apache.org/index.html URL: https://maven.apache.org/index.html Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 2,888: / Line 2,508: @@
 | align="center" | math
 | align="center" | 14.137
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for networks (also known as graphs) based on simulation of (stochastic) flow in graphs. The algorithm was invented/discovered by Stijn van Dongen at the Centre for Mathematics and Computer Science (also known as CWI) in the Netherlands. MCL has been applied in a number of different domains, mostly in bioinformatics. Homepage: http://micans.org/mcl/ Keyword:math<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for networks (also known as graphs) based on simulation of (stochastic) flow in graphs. The algorithm was invented/discovered by Stijn van Dongen at the Centre for Mathematics and Computer Science (also known as CWI) in the Netherlands. MCL has been applied in a number of different domains, mostly in bioinformatics. Homepage: http://micans.org/mcl/ URL: http://micans.org/mcl/ Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [https://www.mathworks.com/products/compiler/mcr/ mcr]
 | align="center" | tools
-| align="center" | R2013a, R2013b, R2014a, R2014b, R2015a, R2015b, R2016a, R2016b, R2017a, R2017b, R2018a, R2018b, R2019a, R2019b, R2020a, R2020b, R2021b, R2022b
+| align="center" | R2020b, R2021b, R2022b
 | Documentation: [[MATLAB]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. Homepage: https://www.mathworks.com/products/compiler/mcr/ URL: https://www.mathworks.com/products/compiler/mcr/ Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 2,902: / Line 2,522: @@
 | align="center" | [https://meep.readthedocs.io/en/latest/ meep]
 | align="center" | phys
-| align="center" | 1.3, 1.16.1, 1.24.0, 1.25.0
+| align="center" | 1.16.1, 1.24.0, 1.25.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Meep is a free and open-source software package for electromagnetics simulation via the finite-difference time-domain (FDTD) method spanning a broad range of applications. Homepage: https://meep.readthedocs.io/en/latest/ URL: https://meep.readthedocs.io/en/latest/ Compatible modules: python/3.8, python/3.9, python/3.10 Keyword:phys<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/nisheth/MeFiT mefit]
-| align="center" | bio
-| align="center" | 1.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MeFiT (Merging and Filtering Tool for Paired-End Reads): This pipeline will merge overlapping paired-end reads, calculate merge statistics, and filter reads for quality. Homepage: https://github.com/nisheth/MeFiT Extensions: HTSeq-0.9.1, pysam-0.14 Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/voutcn/megahit megahit]
 | align="center" | bio
-| align="center" | 1.2.7, 1.2.9
+| align="center" | 1.2.9
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Homepage: https://github.com/voutcn/megahit URL: https://github.com/voutcn/megahit Compatible modules: Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://meme-suite.org meme]
 | align="center" | -
-| align="center" | 4.11.2, 5.0.3, 5.2.0, 5.4.1, 5.5.0, 5.5.5
+| align="center" | 5.2.0, 5.4.1, 5.5.0, 5.5.5
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MEME Suite allows you to: - discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, - search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, - compare a motif to all motifs in a database of motifs, - associate motifs with Gene Ontology terms via their putative target genes, - analyse motif enrichment using SpaMo or CentriMo. Homepage: http://meme-suite.org URL: http://meme-suite.org<br /><br /><br /></div>
-|-
-| align="center" | [http://jgi.doe.gov/data-and-tools/meraculous/ meraculous]
-| align="center" | bio
-| align="center" | 2.2.4
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Distributed and scalable assembler for eukaryotic genomes. Meraculous is a whole genome assembler for Next Generation Sequencing data geared for large genomes. It is a hybrid k-mer/read-based assembler that capitalizes on the high accuracy of Illumina sequence by eschewing an explicit error correction step which we argue to be redundant with the assembly process. Meraculous achieves high performance with large datasets by utilizing lightweight data structures and multi-threaded parallelization, allowing to assemble human-sized genomes on commodity clusters in under a day. The process pipeline implements a highly transparent and portable model of job control and monitoring where different assembly stages can be executed and re-executed separately or in unison on a wide variety of architectures. Homepage: http://jgi.doe.gov/data-and-tools/meraculous/ Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [https://www.mesa3d.org/ mesa]
-| align="center" | vis
-| align="center" | 18.0.0, 18.3.6
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. Homepage: https://www.mesa3d.org/ URL: https://www.mesa3d.org/ Keyword:vis<br /><br /><br /></div>
 |-
 | align="center" | [https://software.sandia.gov/mesquite/ mesquite]
 | align="center" | math
 | align="center" | 2.3.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Mesh-Quality Improvement Library Homepage: https://software.sandia.gov/mesquite/ Keyword:math<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Mesh-Quality Improvement Library Homepage: https://software.sandia.gov/mesquite/ URL: https://software.sandia.gov/mesquite/ Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [https://dtcenter.org/ met]
 | align="center" | phys
-| align="center" | 8.0_bugfix, 9.0.2, 9.1.1
+| align="center" | 9.1.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Model Evaluation Tools (MET) is a highly configurable, state-of-the-art suite of verification tools designed for the verification and evaluation of numerical weather forecasts. Although MET was developed at the Developmental Testbed Center (DTC) to be used with the Weather Research and Forecasting (WRF) modeling system, the data formats and standards used allow MET to be run on the output of other modeling systems as well. Homepage: https://dtcenter.org/ URL: https://dtcenter.org/ Keyword:phys<br /><br /><br /></div>
 |-
-| align="center" | [https://docs.computecanada.ca/wiki/META_package_for_serial_farming meta-farm]
+| align="center" | [https://docs.alliancecan.ca/wiki/META-Farm meta-farm]
 | align="center" | -
 | align="center" | 1.0.2
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Meta-farm is a suite of scripts designed in-house to fully automate throughput computing (running a large number of related serial/parallel/GPU jobs - so called farming). Homepage: https://docs.computecanada.ca/wiki/META_package_for_serial_farming URL: https://docs.computecanada.ca/wiki/META_package_for_serial_farming<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Meta-farm is a suite of scripts designed in-house to fully automate throughput computing (running a large number of related serial/parallel/GPU jobs - so called farming). Homepage: https://docs.alliancecan.ca/wiki/META-Farm URL: https://docs.alliancecan.ca/wiki/META-Farm<br /><br /><br /></div>
 |-
 | align="center" | [https://bitbucket.org/berkeleylab/metabat metabat]
@@ Line 2,968: / Line 2,573: @@
 | align="center" | bio
 | align="center" | 2011-03-25
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: METAL provides a computationally efficient tool for meta-analysis of genome-wide association scans, which is a commonly used approach for improving power complex traits gene mapping studies. METAL provides a rich scripting interface and implements efficient memory management to allow analyses of very large data sets and to support a variety of input file formats. Availability and implementation: METAL, including source code, documentation, examples, and executables, is available at: http://www.sph.umich.edu/csg/abecasis/metal/ If you use Metal please fill out the registration form on the page: http://csg.sph.umich.edu/abecasis/metal/download/ Contact: goncalo@umich.edu Homepage: http://www.sph.umich.edu/csg/abecasis/metal/ Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: METAL provides a computationally efficient tool for meta-analysis of genome-wide association scans, which is a commonly used approach for improving power complex traits gene mapping studies. METAL provides a rich scripting interface and implements efficient memory management to allow analyses of very large data sets and to support a variety of input file formats. Availability and implementation: METAL, including source code, documentation, examples, and executables, is available at: http://www.sph.umich.edu/csg/abecasis/metal/ If you use Metal please fill out the registration form on the page: http://csg.sph.umich.edu/abecasis/metal/download/ Contact: goncalo@umich.edu Homepage: http://www.sph.umich.edu/csg/abecasis/metal/ URL: http://www.sph.umich.edu/csg/abecasis/metal/ Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/DiltheyLab/MetaMaps metamaps]
-| align="center" | -
-| align="center" | 2020.03.11
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MetaMaps is tool specifically developed for the analysis of long-read (PacBio/Oxford Nanopore) metagenomic datasets. It simultaenously carries out read assignment and sample composition estimation. It is faster than classical exact alignment-based approaches, and its output is more information-rich than that of kmer-spectra-based methods. For example, each MetaMaps alignment comes with an approximate alignment location, an estimated alignment identity and a mapping quality. The approximate mapping algorithm employed by MetaMaps is based on MashMap. MetaMaps adds a mapping quality model and EM-based estimation of sample composition. Homepage: https://github.com/DiltheyLab/MetaMaps URL: https://github.com/DiltheyLab/MetaMaps<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/biobakery/MetaPhlAn metaphlan]
-| align="center" | bio
-| align="center" | 2.2.0, 2.8
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. Homepage: https://github.com/biobakery/MetaPhlAn URL: https://github.com/biobakery/MetaPhlAn Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://microbiology.se/software/metaxa2/ metaxa2]
@@ Line 2,992: / Line 2,587: @@
 | align="center" | [http://glaros.dtc.umn.edu/gkhome/metis/metis/overview metis]
 | align="center" | math
-| align="center" | 4.0.3, 5.1.0
+| align="center" | 5.1.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. Homepage: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview URL: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview Keyword:math<br /><br /><br /></div>
 |-
@@ Line 2,999: / Line 2,594: @@
 | align="center" | 5.1.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. Homepage: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview URL: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview<br /><br /><br /></div>
-|-
-| align="center" | [http://mfem.org/ mfem]
-| align="center" | phys
-| align="center" | 3.4
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MFEM is a free, lightweight, scalable C++ library for finite element methods. Homepage: http://mfem.org/ Keyword:phys<br /><br /><br /></div>
 |-
 | align="center" | [http://popgen.sc.fsu.edu/Migrate/Migrate-n.html migrate-n]
@@ Line 3,017: / Line 2,607: @@
 | align="center" | [http://bic-mni.github.io/ minc-toolkit]
 | align="center" | bio
-| align="center" | 1.9.16, 1.9.18.1, 1.9.18.3
+| align="center" | 1.9.18.1, 1.9.18.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Medical Imaging NetCDF Toolkit Homepage: http://bic-mni.github.io/ URL: http://bic-mni.github.io/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/GATB/gatb-core minia]
 | align="center" | bio
-| align="center" | 2.0.7, 3.2.6
+| align="center" | 3.2.6
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GATB - The Genome Analysis Toolbox with de-Bruijn graph. Homepage: https://github.com/GATB/gatb-core URL: https://github.com/GATB/gatb-core Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 3,029: / Line 2,619: @@
 | align="center" | 0.3-20191007
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. It simply concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to the raw input reads. Homepage: https://github.com/lh3/minimap2 URL: https://github.com/lh3/minimap2 Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://genome.sph.umich.edu/wiki/Minimac2 minimac2]
-| align="center" | bio
-| align="center" | 2014.9.15
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: minimac2 is an improved version of Minimac. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. The name has two parts. The first, mini, refers to the modest amount of computational resources it requires. The second, mac, is short hand for MaCH, our widely used algorithm for genotype imputation. - Homepage: http://genome.sph.umich.edu/wiki/Minimac2 Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://genome.sph.umich.edu/wiki/Minimac3 minimac3]
 | align="center" | bio
 | align="center" | 2.0.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Minimac3 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac and minimac2. Minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy. Homepage: http://genome.sph.umich.edu/wiki/Minimac3 Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Minimac3 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac and minimac2. Minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy. Homepage: http://genome.sph.umich.edu/wiki/Minimac3 URL: http://genome.sph.umich.edu/wiki/Minimac3 Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://genome.sph.umich.edu/wiki/Minimac4 minimac4]
@@ Line 3,047: / Line 2,632: @@
 | align="center" | [https://github.com/lh3/minimap2 minimap2]
 | align="center" | bio
-| align="center" | 2.13, 2.17, 2.18, 2.24, 2.26, 2.28
+| align="center" | 2.17, 2.18, 2.24, 2.26, 2.28
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment. Homepage: https://github.com/lh3/minimap2 URL: https://github.com/lh3/minimap2 Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 3,054: / Line 2,639: @@
 | align="center" | 1.6
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset. Homepage: https://omics.informatics.indiana.edu/MinPath URL: https://omics.informatics.indiana.edu/MinPath<br /><br /><br /></div>
-|-
-| align="center" | [https://sourceforge.net/projects/mira-assembler/ mira]
-| align="center" | bio
-| align="center" | 4.0.2
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the latter at the moment only CCS and error-corrected CLR reads). Homepage: https://sourceforge.net/projects/mira-assembler/ Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://nar.oxfordjournals.org/content/41/13/e129 mitobim]
-| align="center" | bio
-| align="center" | 1.9
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This document contains instructions on how to use the MITObim pipeline described in Hahn et al. 2013. The full article c an be found [here](http://nar.oxfordjournals.org/content/41/13/e129 "MITObim full article at NAR"). Kindly cite the arti cle if you are using MITObim in your work. Homepage: https://github.com/chrishah/MITObim/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://mixcr.readthedocs.io/en/latest/quickstart.html mixcr]
 | align="center" | bio
-| align="center" | 2.1.5, 2.1.10, 3.0.13, 4.1.2
+| align="center" | 4.1.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MiXCR is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR errors and identifies germline hypermutations. The software supports both partial- and full-length profiling and employs all available RNA or DNA information, including sequences upstream of V and downstream of J gene segments. Homepage: http://mixcr.readthedocs.io/en/latest/quickstart.html URL: http://mixcr.readthedocs.io/en/latest/quickstart.html Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [https://01.org/mkl-dnn mkl-dnn]
-| align="center" | ai
-| align="center" | 0.16
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL-DNN) Homepage: https://01.org/mkl-dnn Keyword:ai<br /><br /><br /></div>
 |-
 | align="center" | [https://mmseqs.com mmseqs2]
 | align="center" | -
-| align="center" | 10-6d92c, 14-7e284, 15-6f452, 13-45111
+| align="center" | 15-6f452, 14-7e284, 13-45111
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MMseqs2: ultra fast and sensitive search and clustering suite Homepage: https://mmseqs.com URL: https://mmseqs.com<br /><br /><br /></div>
 |-
@@ Line 3,087: / Line 2,657: @@
 | align="center" | [http://www.cmbi.ru.nl/molden/ molden]
 | align="center" | chem
-| align="center" | 5.7, 6.5
+| align="center" | 6.5
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac Homepage: http://www.cmbi.ru.nl/molden/ URL: http://www.cmbi.ru.nl/molden/ Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://www.mono-project.com/ mono]
 | align="center" | tools
-| align="center" | 4.6.2.7, 5.16.0.179, 6.12.0.122
+| align="center" | 6.12.0.122
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET. Homepage: https://www.mono-project.com/ URL: https://www.mono-project.com/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [http://www.mothur.org/ mothur]
 | align="center" | bio
-| align="center" | 1.40.4, 1.41.0, 1.41.1, 1.41.3, 1.44.3, 1.46.1, 1.47.0, 1.48.0
+| align="center" | 1.44.3, 1.46.1, 1.47.0, 1.48.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. Homepage: http://www.mothur.org/ URL: http://www.mothur.org/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 3,114: / Line 2,684: @@
 | align="center" | 1.11.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MPB is a software package to compute definite-frequency eigenstates of Maxwell's equations in periodic dielectric structures. It can compute optical dispersion relations and eigenstates for structures such as strip waveguides and optical fibers. MPB is well suited for the study of photonic crystals: periodic dielectric structures exhibiting a band gap in their optical modes, prohibiting propagation of light in that frequency range. Homepage: https://mpb.readthedocs.io/en/latest URL: https://mpb.readthedocs.io/en/latest<br /><br /><br /></div>
-|-
-| align="center" | [http://www.mcs.anl.gov/research/projects/perfvis/download/index.htm mpe2]
-| align="center" | mpi
-| align="center" | 2.4.9b
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MPE is a software package for MPI (Message Passing Interface) programmers. The package provides users with a number of useful tools for their MPI programs. The latest version is called MPE2. Current available tools under MPE2 are the following: 1. A set of profiling libraries to collect information about the behavior of MPI programs. Linking the user MPI program with the libraries will generate logfile for postmortem visualization when the user program is executed. 2. Convenient compiler wrapper, mpecc and mpefc, are provided to compile/link with the related profiled libraries, e.g. "mpecc -mpilog" enables automatic MPI and user-defined MPE logging, "mpecc -mpicheck" enables collective and datatype checking of the user MPI program, and "mpecc -help" shows available options. 3. A SLOG-2 viewer, Jumpshot, for the various logfiles. 4. A set of CLOG-2 and SLOG-2 utilities programs. 5. An MPI collective and datatype checking library. 6. A shared-display parallel X graphics library. 7. A profiling wrapper generator for MPI interface. 8. Routines for sequentializing a section of code being executed in parallel. 9. Debugger setup routines. Homepage: http://www.mcs.anl.gov/research/projects/perfvis/download/index.htm Keyword:mpi<br /><br /><br /></div>
-|-
-| align="center" | [http://perso.ens-lyon.fr/nathalie.revol/software.html mpfi]
-| align="center" | math
-| align="center" | 1.5.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MPFI, a multiple precision interval arithmetic library based on MPFR MPFI stands for Multiple Precision Floating-point Interval library. Homepage: http://perso.ens-lyon.fr/nathalie.revol/software.html Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [https://bitbucket.org/mpi4py/mpi4py mpi4py]
 | align="center" | tools
-| align="center" | 3.0.0, 3.0.3, 3.1.2, 3.1.3, 3.1.4, 3.1.6
+| align="center" | 3.0.3, 3.1.2, 3.1.3, 3.1.4, 3.1.6
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors. Homepage: https://bitbucket.org/mpi4py/mpi4py URL: https://bitbucket.org/mpi4py/mpi4py Compatible modules: python/3.10, python/3.11, python/3.12 Keyword:tools<br /><br /><br /></div>
-|-
-| align="center" | [http://www.mpich.org/ mpich]
-| align="center" | -
-| align="center" | 3.2.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices). Homepage: http://www.mpich.org/<br /><br /><br /></div>
 |-
 | align="center" | [https://numpi.dm.unipi.it/software/mpsolve mpsolve]
@@ Line 3,142: / Line 2,697: @@
 | align="center" | [https://nbisweden.github.io/MrBayes/ mrbayes]
 | align="center" | bio
-| align="center" | 3.2.6, 3.2.7a
+| align="center" | 3.2.7
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. Homepage: https://nbisweden.github.io/MrBayes/ URL: https://nbisweden.github.io/MrBayes/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 3,152: / Line 2,707: @@
 | align="center" | [http://www.brain.org.au/software/index.html#mrtrix mrtrix]
 | align="center" | bio
-| align="center" | 3.0_RC3, 3.0.1
+| align="center" | 3.0.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines. Homepage: http://www.brain.org.au/software/index.html#mrtrix URL: http://www.brain.org.au/software/index.html#mrtrix Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 3,158: / Line 2,713: @@
 | align="center" | chem
 | align="center" | 1.7.3.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Multiscale Coarse-Graining (MS-CG) method is a variational force-matching technique developed by the Voth group. This project serves as the workhorse implementation of the method used as a standard force-matching code. The development of MS-CG is supported by academic research grants. If you use this package, please cite at least one of these papers: - S. Izvekov and G. A. Voth, J. Chem. Phys. 123, 134105 (2005). - W. G. Noid, et al., J. Chem. Phys. 128, 244114 (2008). - W. G. Noid et al., J. Chem. Phys. 128, 244115 (2008). - L. Lu, S. Izvekov, A. Das, H. C. Andersen, and G. A. Voth, Journal of Chemical Theory and Computation, 6(3), 954-965 (2010). Homepage: https://github.com/uchicago-voth/MSCG-release Keyword:chem<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Multiscale Coarse-Graining (MS-CG) method is a variational force-matching technique developed by the Voth group. This project serves as the workhorse implementation of the method used as a standard force-matching code. The development of MS-CG is supported by academic research grants. If you use this package, please cite at least one of these papers: - S. Izvekov and G. A. Voth, J. Chem. Phys. 123, 134105 (2005). - W. G. Noid, et al., J. Chem. Phys. 128, 244114 (2008). - W. G. Noid et al., J. Chem. Phys. 128, 244115 (2008). - L. Lu, S. Izvekov, A. Das, H. C. Andersen, and G. A. Voth, Journal of Chemical Theory and Computation, 6(3), 954-965 (2010). Homepage: https://github.com/uchicago-voth/MSCG-release URL: https://github.com/uchicago-voth/MSCG-release Keyword:chem<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/stschiff/msmc msmc]
-| align="center" | bio
-| align="center" | 1.0.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This software implements MSMC, a method to infer population size and gene flow from multiple genome sequences (Schiffels and Durbin, 2014, Nature Genetics, or Preprint). In short, msmc can infer the scaled population size of a single population as a function of time the timing and nature of population separations between two populations from multiple phased haplotypes. When only two haplotypes are given, MSMC is similar to PSMC, and we call it PSMC' because of subtle differences in the method and the underlying model, which allows PSMC' to infer more accurately the recombination rate. Homepage: https://github.com/stschiff/msmc Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/stschiff/msmc msmc2]
 | align="center" | -
-| align="center" | 2.0.0, 2.1.3
+| align="center" | 2.1.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This program implements MSMC2, a method to infer population size history and population separation history from whole genome sequencing data. For a general guide, please refer to version 1: https://github.com/stschiff/msmc Binaries are attached to the releases (under the "Releases" tab within github). Homepage: https://github.com/stschiff/msmc URL: https://github.com/stschiff/msmc<br /><br /><br /></div>
 |-
@@ Line 3,184: / Line 2,734: @@
 | align="center" | 1.0.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: generate multiset combinations (n multichoose k). Homepage: https://github.com/ekg/multichoose URL: https://github.com/ekg/multichoose<br /><br /><br /></div>
-|-
-| align="center" | [http://sobereva.com/multiwfn/ multiwfn]
-| align="center" | chem
-| align="center" | 3.5, 3.6
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A multifunctional wavefunction analyzer. Homepage: http://sobereva.com/multiwfn/ Keyword:chem<br /><br /><br /></div>
-|-
-| align="center" | [https://sourceforge.net/projects/multovl/ multovl]
-| align="center" | bio
-| align="center" | 1.3.8203e7d
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MULTOVL suite of programs finds multiple overlaps among genomic regions. The MULTOVL algorithm can detect several kinds of region overlaps. In addition to the N-fold overlaps you can detect solitary regions which are the input regions that do not overlap with any other region in the input data set, and union overlaps that is the union of the input regions that overlap at least once somewhere. Homepage: https://sourceforge.net/projects/multovl/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://mummer.sourceforge.net/ mummer]
 | align="center" | bio
-| align="center" | 3.23, 4.0.0beta2
+| align="center" | 4.0.0beta2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. Homepage: http://mummer.sourceforge.net/ URL: http://mummer.sourceforge.net/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://graal.ens-lyon.fr/MUMPS/ mumps-metis]
 | align="center" | tools
-| align="center" | 5.1.2, 5.2.1
+| align="center" | 5.2.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A parallel sparse direct solver Homepage: https://graal.ens-lyon.fr/MUMPS/ URL: https://graal.ens-lyon.fr/MUMPS/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [http://graal.ens-lyon.fr/MUMPS/ mumps-parmetis]
 | align="center" | tools
-| align="center" | 5.1.2, 5.3.5
+| align="center" | 5.3.5
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A parallel sparse direct solver Homepage: http://graal.ens-lyon.fr/MUMPS/ URL: http://graal.ens-lyon.fr/MUMPS/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [http://beltoforion.de/article.php?a=muparser muparser]
 | align="center" | math
-| align="center" | 2.2.5, 2.2.6, 2.3.2
+| align="center" | 2.2.5, 2.3.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: muParser is an extensible high performance math expression parser library written in C++. It works by transforming a mathematical expression into bytecode and precalculating constant parts of the expression. Homepage: http://beltoforion.de/article.php?a=muparser URL: http://beltoforion.de/article.php?a=muparser Keyword:math<br /><br /><br /></div>
 |-
@@ Line 3,222: / Line 2,762: @@
 | align="center" | [https://drive5.com/muscle/ muscle]
 | align="center" | bio
-| align="center" | 3.8.31, 3.8.1551
+| align="center" | 3.8.1551
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes-only a handful of command-line options are needed to perform common alignment tasks. Homepage: https://drive5.com/muscle/ URL: https://drive5.com/muscle/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 3,229: / Line 2,769: @@
 | align="center" | 5.7.36, 8.3.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MySQL is one of the world's most widely used open-source relational database management system (RDBMS). Homepage: http://www.mysql.com/ URL: http://www.mysql.com/ Keyword:tools<br /><br /><br /></div>
-|-
-| align="center" | [http://www.ks.uiuc.edu/Research/namd/ namd-mpi]
-| align="center" | chem
-| align="center" | 2.13
-| Documentation: [[NAMD]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Homepage: http://www.ks.uiuc.edu/Research/namd/ Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [http://www.ks.uiuc.edu/Research/namd/ namd-multicore]
 | align="center" | chem
-| align="center" | 2.13, 2.14
+| align="center" | 2.14
 | Documentation: [[NAMD]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Homepage: http://www.ks.uiuc.edu/Research/namd/ URL: http://www.ks.uiuc.edu/Research/namd/ Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 3,252: / Line 2,787: @@
 | align="center" | [http://www.ks.uiuc.edu/Research/namd/ namd-ucx]
 | align="center" | chem
-| align="center" | 2.13, 2.14
+| align="center" | 2.14
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Homepage: http://www.ks.uiuc.edu/Research/namd/ URL: http://www.ks.uiuc.edu/Research/namd/ Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 3,259: / Line 2,794: @@
 | align="center" | 2.14
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Homepage: http://www.ks.uiuc.edu/Research/namd/ URL: http://www.ks.uiuc.edu/Research/namd/<br /><br /><br /></div>
-|-
-| align="center" | [http://www.ks.uiuc.edu/Research/namd/ namd-verbs]
-| align="center" | chem
-| align="center" | 2.13
-| Documentation: [[NAMD]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Homepage: http://www.ks.uiuc.edu/Research/namd/ Keyword:chem<br /><br /><br /></div>
-|-
-| align="center" | [http://www.ks.uiuc.edu/Research/namd/ namd-verbs-smp]
-| align="center" | chem
-| align="center" | 2.13
-| Documentation: [[NAMD]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Homepage: http://www.ks.uiuc.edu/Research/namd/ Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/jlblancoc/nanoflann nanoflann]
@@ Line 3,277: / Line 2,802: @@
 | align="center" | [https://github.com/jts/nanopolish nanopolish]
 | align="center" | bio
-| align="center" | 0.8.5, 0.11.2, 0.13.2
+| align="center" | 0.11.2, 0.13.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more. Homepage: https://github.com/jts/nanopolish URL: https://github.com/jts/nanopolish Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 3,287: / Line 2,812: @@
 | align="center" | [https://developer.nvidia.com/nccl nccl]
 | align="center" | tools
-| align="center" | 2.3.5, 2.4.2, 2.5.6, 2.7.8, 2.8.4, 2.11.4, 2.12.12, 2.18.3, 2.18.5
+| align="center" | 2.7.8, 2.8.4, 2.11.4, 2.12.12, 2.18.3, 2.18.5
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs. Homepage: https://developer.nvidia.com/nccl URL: https://developer.nvidia.com/nccl Keyword:tools<br /><br /><br /></div>
-|-
-| align="center" | [https://gitlab.com/remikz/nccmp nccmp]
-| align="center" | -
-| align="center" | 1.8.7.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: nccmp compares two NetCDF files bitwise, semantically or with a user defined tolerance (absolute or relative percentage). Parallel comparisons are done in local memory without requiring temporary files. Highly recommended for regression testing scientific models or datasets in a test-driven development environment. Homepage: https://gitlab.com/remikz/nccmp URL: https://gitlab.com/remikz/nccmp<br /><br /><br /></div>
 |-
 | align="center" | [https://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html nciplot]
@@ Line 3,300: / Line 2,820: @@
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NCIPLOT is a program for revealing non covalent interactions based on the reduced density gradient. Homepage: https://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html URL: https://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html<br /><br /><br /></div>
 |-
-| align="center" | [http://www.ncl.ucar.edu ncl]
+| align="center" | [https://www.ncl.ucar.edu ncl]
 | align="center" | vis
 | align="center" | 6.6.2
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NCL is an interpreted language designed specifically for scientific data analysis and visualization. Homepage: http://www.ncl.ucar.edu URL: http://www.ncl.ucar.edu Keyword:vis<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NCL is an interpreted language designed specifically for scientific data analysis and visualization. Homepage: https://www.ncl.ucar.edu URL: https://www.ncl.ucar.edu Keyword:vis<br /><br /><br /></div>
 |-
 | align="center" | [https://nco.sourceforge.net nco]
 | align="center" | io
-| align="center" | 4.6.6, 4.9.5, 5.0.6, 5.1.7
+| align="center" | 4.9.5, 5.0.6, 5.1.7
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5 Homepage: https://nco.sourceforge.net URL: https://nco.sourceforge.net Keyword:io<br /><br /><br /></div>
 |-
 | align="center" | [http://meteora.ucsd.edu/~pierce/ncview_home_page.html ncview]
 | align="center" | vis
-| align="center" | 2.1.7, 2.1.8
+| align="center" | 2.1.8
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. Homepage: http://meteora.ucsd.edu/~pierce/ncview_home_page.html URL: http://meteora.ucsd.edu/~pierce/ncview_home_page.html Keyword:vis<br /><br /><br /></div>
 |-
 | align="center" | [https://www.nektar.info/ nektar++]
 | align="center" | math
-| align="center" | 4.4.1, 5.0.1, 5.3.0
+| align="center" | 5.0.1, 5.3.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Nektar++ is a tensor product based finite element package designed to allow one to construct efficient classical low polynomial order h-type solvers (where h is the size of the finite element) as well as higher p-order piecewise polynomial order solvers. Homepage: https://www.nektar.info/ URL: https://www.nektar.info/ Keyword:math<br /><br /><br /></div>
-|-
-| align="center" | [http://neper.sourceforge.net/index.html neper]
-| align="center" | chem
-| align="center" | 3.3.0, 3.4.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Neper is a software package for polycrystal generation and meshing. It can deal with 2D and 3D polycrystals with very large numbers of grains. Homepage: http://neper.sourceforge.net/index.html Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://www.unidata.ucar.edu/software/netcdf/ netcdf]
 | align="center" | io
-| align="center" | 4.6.1, 4.7.0, 4.7.3, 4.7.4, 4.8.0, 4.9.0, 4.9.2
+| align="center" | 4.7.4, 4.8.0, 4.9.0, 4.9.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Compatible modules: python/3.10, python/3.10, python/3.11, python/3.11, python/3.10, python/3.10, python/3.11, python/3.11 Extensions: certifi-2023.7.22, cftime-1.6.2, netCDF4-1.6.4 Keyword:io<br /><br /><br /></div>
-|-
-| align="center" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-c++]
-| align="center" | io
-| align="center" | 4.2
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io<br /><br /><br /></div>
 |-
 | align="center" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-c++-mpi]
 | align="center" | io
 | align="center" | 4.2
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: http://www.unidata.ucar.edu/software/netcdf/ URL: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io<br /><br /><br /></div>
 |-
 | align="center" | [https://www.unidata.ucar.edu/software/netcdf/ netcdf-c++4]
 | align="center" | io
-| align="center" | 4.3.0, 4.3.1
+| align="center" | 4.3.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Keyword:io<br /><br /><br /></div>
 |-
 | align="center" | [https://www.unidata.ucar.edu/software/netcdf/ netcdf-c++4-mpi]
 | align="center" | io
-| align="center" | 4.3.0, 4.3.1
+| align="center" | 4.3.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Keyword:io<br /><br /><br /></div>
 |-
 | align="center" | [https://www.unidata.ucar.edu/software/netcdf/ netcdf-fortran]
 | align="center" | io
-| align="center" | 4.4.4, 4.4.5, 4.5.2, 4.5.3, 4.6.0, 4.6.1
+| align="center" | 4.5.2, 4.5.3, 4.6.0, 4.6.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Keyword:io<br /><br /><br /></div>
 |-
 | align="center" | [https://www.unidata.ucar.edu/software/netcdf/ netcdf-fortran-mpi]
 | align="center" | io
-| align="center" | 4.4.4, 4.5.1, 4.5.2, 4.5.3, 4.6.0, 4.6.1
+| align="center" | 4.5.2, 4.5.3, 4.6.0, 4.6.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Keyword:io<br /><br /><br /></div>
 |-
 | align="center" | [https://www.unidata.ucar.edu/software/netcdf/ netcdf-mpi]
 | align="center" | io
-| align="center" | 4.4.1.1, 4.6.1, 4.7.4, 4.8.0, 4.8.1, 4.9.0, 4.9.2
+| align="center" | 4.7.4, 4.8.0, 4.8.1, 4.9.0, 4.9.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Compatible modules: python/3.10, python/3.10, python/3.11, python/3.11, python/3.10, python/3.10, python/3.11, python/3.11 Extensions: certifi-2023.7.22, cftime-1.6.2, netCDF4-1.6.4 Keyword:io<br /><br /><br /></div>
-|-
-| align="center" | [http://www.lysator.liu.se/~nisse/nettle/ nettle]
-| align="center" | -
-| align="center" | 3.3
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space. Homepage: http://www.lysator.liu.se/~nisse/nettle/<br /><br /><br /></div>
-|-
-| align="center" | [http://python.org/ networkx]
-| align="center" | tools
-| align="center" | 1.1, 2.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bundle which contains networkx for different Python versions Homepage: http://python.org/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [http://www.neuron.yale.edu/neuron neuron]
@@ Line 3,382: / Line 2,882: @@
 | align="center" | [http://www.robertnz.net/index.html newmat]
 | align="center" | -
-| align="center" | 10, 11
+| align="center" | 11
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Newmat C++ library is intended for scientists and engineers who need to manipulate a variety of types of matrices using standard matrix operations. Emphasis is on the kind of operations needed in statistical calculations such as least squares, linear equation solve and eigenvalues. Homepage: http://www.robertnz.net/index.html URL: http://www.robertnz.net/index.html<br /><br /><br /></div>
 |-
@@ Line 3,392: / Line 2,892: @@
 | align="center" | [https://www.nextflow.io/ nextflow]
 | align="center" | -
-| align="center" | 19.04.0, 19.10.0, 20.04.1, 20.10.0, 21.04.3, 21.10.3, 22.04.3, 22.10.6, 22.10.8, 23.04.3, 23.10.0
+| align="center" | 20.10.0, 21.04.3, 21.10.3, 22.04.3, 22.10.6, 22.10.8, 23.04.3, 23.10.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data Homepage: https://www.nextflow.io/ URL: https://www.nextflow.io/<br /><br /><br /></div>
 |-
 | align="center" | [http://cibiv.github.io/NextGenMap/ nextgenmap]
 | align="center" | bio
-| align="center" | 0.5.0, 0.5.5
+| align="center" | 0.5.5
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. Homepage: http://cibiv.github.io/NextGenMap/ URL: http://cibiv.github.io/NextGenMap/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 3,414: / Line 2,914: @@
 | align="center" | 2.10.5
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. Homepage: https://github.com/ncbi/ngs URL: https://github.com/ncbi/ngs<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/imgag/ngs-bits ngs-bits]
-| align="center" | bio
-| align="center" | 2018_10
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ngs-bits contains a lot of tools that are used for NGS-based diagnostics Homepage: https://github.com/imgag/ngs-bits Extensions: kiwisolver-1.0.1, matplotlib-3.0.2, pyparsing-2.3.0, subprocess32-3.5.3 Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/mfumagalli/ngsTools ngstools]
-| align="center" | bio
-| align="center" | 1.0.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ngsTools is a collection of programs for population genetics analyses from NGS data, taking into account data statistical uncertainty. The methods implemented in these programs do not rely on SNP or genotype calling, and are particularly suitable for low sequencing depth data. An application note illustrating its application has published (Fumagalli et al., 2014). Homepage: https://github.com/mfumagalli/ngsTools Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/yahoojapan/NGT ngt]
@@ Line 3,434: / Line 2,924: @@
 | align="center" | 5.2.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NiBabel provides read/write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI. Homepage: https://nipy.github.io/nibabel URL: https://nipy.github.io/nibabel Compatible modules: python/3.10, python/3.11 Extensions: bz2file-0.98, nibabel-5.2.0, pydicom-2.4.4<br /><br /><br /></div>
-|-
-| align="center" | [https://ninja-build.org/ ninja]
-| align="center" | -
-| align="center" | 1.9.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Ninja is a small build system with a focus on speed. Homepage: https://ninja-build.org/ URL: https://ninja-build.org/<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/TravisWheelerLab/NINJA ninja-phylogenetics]
@@ Line 3,447: / Line 2,932: @@
 | align="center" | [http://ab-initio.mit.edu/wiki/index.php/NLopt nlopt]
 | align="center" | math
-| align="center" | 2.4.2, 2.6.1, 2.6.2, 2.7.0, 2.7.1
+| align="center" | 2.6.1, 2.6.2, 2.7.0, 2.7.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. Homepage: http://ab-initio.mit.edu/wiki/index.php/NLopt URL: http://ab-initio.mit.edu/wiki/index.php/NLopt Compatible modules: python/3.10, python/3.10, python/3.10, python/3.10, python/3.11, python/3.11, python/3.11, python/3.11 Keyword:math<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. Homepage: http://ab-initio.mit.edu/wiki/index.php/NLopt URL: http://ab-initio.mit.edu/wiki/index.php/NLopt Compatible modules: python/3.8, python/3.9, python/3.10 Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [https://nodejs.org nodejs]
 | align="center" | tools
-| align="center" | 11.1.0, 12.16.1, 14.4.0, 15.2.1, 18.17.1
+| align="center" | 12.16.1, 15.2.1, 18.17.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices. Homepage: https://nodejs.org URL: https://nodejs.org Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR nspr]
 | align="center" | -
-| align="center" | 4.21, 4.25
+| align="center" | 4.25
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. Homepage: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR URL: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR<br /><br /><br /></div>
 |-
 | align="center" | [https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS nss]
 | align="center" | -
-| align="center" | 3.45, 3.51
+| align="center" | 3.51
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. Homepage: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS URL: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS<br /><br /><br /></div>
 |-
@@ Line 3,472: / Line 2,957: @@
 | align="center" | [http://www.shoup.net/ntl/ ntl]
 | align="center" | math
-| align="center" | 11.3.0, 11.4.3
+| align="center" | 11.4.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NTL is a high-performance, portable C++ library providing data structures and algorithms for manipulating signed, arbitrary length integers, and for vectors, matrices, and polynomials over the integers and over finite fields. Homepage: http://www.shoup.net/ntl/ URL: http://www.shoup.net/ntl/ Keyword:math<br /><br /><br /></div>
-|-
-| align="center" | [https://william-dawson.github.io/NTPoly/ ntpoly]
-| align="center" | -
-| align="center" | 2.2
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NTPoly is a massively parallel library for computing the functions of sparse, symmetric matrices based on polynomial expansions. Homepage: https://william-dawson.github.io/NTPoly/<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/NVlabs/nvbio nvbio]
@@ Line 3,489: / Line 2,969: @@
 | align="center" | 20.7, 22.1, 22.7, 23.7, 23.9
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI) Homepage: https://developer.nvidia.com/hpc-sdk/ URL: https://developer.nvidia.com/hpc-sdk/<br /><br /><br /></div>
-|-
-| align="center" | [https://gcc.gnu.org/wiki/nvptx nvptx-tools]
-| align="center" | -
-| align="center" | 0.20180301
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A collection of tools for use with nvptx-none GCC toolchains: https://gcc.gnu.org/wiki/nvptx Homepage: https://github.com/MentorEmbedded/nvptx-tools URL: https://github.com/MentorEmbedded/nvptx-tools<br /><br /><br /></div>
 |-
 | align="center" | [http://www.nwchem-sw.org nwchem]
 | align="center" | chem
-| align="center" | 6.6.revision27746, 7.0.2-p1, 6.8.1
+| align="center" | 7.0.2-p1, 6.8.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. Homepage: http://www.nwchem-sw.org URL: http://www.nwchem-sw.org Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 3,504: / Line 2,979: @@
 | align="center" | 0.2.09
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. Homepage: https://github.com/dzerbino/oases URL: https://github.com/dzerbino/oases<br /><br /><br /></div>
-|-
-| align="center" | [http://www.oasys-software.com/dyna/en/ oasys-ls-dyna]
-| align="center" | phys
-| align="center" | 14.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Oasys Suite of software, exclusively written for LS-DYNA, is at the leading edge of the pre- and post-processing markets and is used worldwide by many of the largest LS-DYNA customers. Homepage: http://www.oasys-software.com/dyna/en/ Keyword:phys<br /><br /><br /></div>
 |-
 | align="center" | [https://www.opencascade.com/ occt]
@@ Line 3,517: / Line 2,987: @@
 | align="center" | [https://www.gnu.org/software/octave/ octave]
 | align="center" | tools
-| align="center" | 4.2.2, 5.2.0, 7.2.0
+| align="center" | 5.2.0, 7.2.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GNU Octave is a high-level interpreted language, primarily intended for numerical computations. Homepage: https://www.gnu.org/software/octave/ URL: https://www.gnu.org/software/octave/ Extensions: control-3.5.0, general-2.1.3, io-2.6.4, optim-1.6.2, signal-1.4.5, statistics-1.4.3, struct-1.0.18 Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page octopus]
 | align="center" | chem
-| align="center" | 7.2, 9.1, 10.1
+| align="center" | 10.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation. Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page URL: http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 3,554: / Line 3,024: @@
 | align="center" | 2.0.5
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface. Homepage: https://www.score-p.org URL: https://www.score-p.org<br /><br /><br /></div>
-|-
-| align="center" | [http://open3dqsar.sourceforge.net/?Home open3dqsar]
-| align="center" | chem
-| align="center" | 2.3
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Open3DQSAR is an open-source tool aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs). Open3DQSAR can generate steric potential, electron density and MM/QM electrostatic potential fields; furthermore, it can import GRIDKONT binary files produced by GRID, CoMFA/CoMSIA fields (exported from SYBYL with the aid of a small SPL script), and MOE grid interaction fields (exported from and MOE with the aid of a small SVL script). Homepage: http://open3dqsar.sourceforge.net/?Home Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://openbabel.org openbabel]
 | align="center" | chem
-| align="center" | 2.4.1, 3.0.0, 3.1.1
+| align="center" | 3.1.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Homepage: https://openbabel.org URL: https://openbabel.org Compatible modules: python/3.10, python/3.11 Extensions: openbabel-3.1.1.1 Keyword:chem<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Homepage: https://openbabel.org URL: https://openbabel.org Compatible modules: python/3.6, python/3.7, python/3.8, python/3.9, python/3.10, python/3.11 Extensions: openbabel-3.1.1.1 Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://openbabel.org openbabel-omp]
@@ Line 3,572: / Line 3,037: @@
 | align="center" | [http://www.openblas.net/ openblas]
 | align="center" | math
-| align="center" | 0.2.20, 0.3.4, 0.3.6, 0.3.9, 0.3.17, 0.3.18, 0.3.20, 0.3.24
+| align="center" | 0.3.9, 0.3.17, 0.3.18, 0.3.20, 0.3.24
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. Homepage: http://www.openblas.net/ URL: http://www.openblas.net/ Keyword:math<br /><br /><br /></div>
-|-
-| align="center" | [http://xianyi.github.com/OpenBLAS/ openblas-64bits]
-| align="center" | -
-| align="center" | 0.3.9
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. This build is for ILP64 (64bit integer ingexes). Homepage: http://xianyi.github.com/OpenBLAS/ URL: http://xianyi.github.com/OpenBLAS/<br /><br /><br /></div>
 |-
 | align="center" | [https://opencarp.org opencarp]
@@ Line 3,597: / Line 3,057: @@
 | align="center" | [http://opencolorio.org/ opencolorio]
 | align="center" | vis
-| align="center" | 1.0.9, 1.1.1, 2.2.1, 2.3.0
+| align="center" | 1.1.1, 2.2.1, 2.3.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenColorIO (OCIO) is a complete color management solution geared towards motion picture production with an emphasis on visual effects and computer animation. Homepage: http://opencolorio.org/ URL: http://opencolorio.org/ Compatible modules: python/3.11, python/3.10 Keyword:vis<br /><br /><br /></div>
 |-
 | align="center" | [http://opencv.org/ opencv]
 | align="center" | vis
-| align="center" | 3.4.3, 4.1.0, 4.2.0, 4.4.0, 4.5.1, 4.5.5, 4.6.0, 4.7.0, 4.8.0, 4.8.1, 4.9.0, 4.10.0
+| align="center" | 4.4.0, 4.5.1, 4.5.5, 4.6.0, 4.7.0, 4.8.0, 4.8.1, 4.9.0, 4.10.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Homepage: http://opencv.org/ URL: http://opencv.org/ Compatible modules: python/3.10, python/3.11, python/3.12 Keyword:vis<br /><br /><br /></div>
-|-
-| align="center" | [http://opencv.org/ opencv_contrib]
-| align="center" | vis
-| align="center" | 3.4.3
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Homepage: http://opencv.org/ Keyword:vis<br /><br /><br /></div>
 |-
 | align="center" | [https://www.openexr.com/ openexr]
 | align="center" | vis
-| align="center" | 2.2.1, 2.5.2, 3.1.5
+| align="center" | 2.5.2, 3.1.5
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light and Magic for use in computer imaging applications Homepage: https://www.openexr.com/ URL: https://www.openexr.com/ Keyword:vis<br /><br /><br /></div>
 |-
@@ Line 3,622: / Line 3,077: @@
 | align="center" | [https://www.openfoam.com/ openfoam]
 | align="center" | phys
-| align="center" | 2.2.2, 2.3.1, 3.0.1, 4.1, 5.0, 6.20180813, 7, 9, 10, v1712, v1812, v1906, v1912, v2006, v2012, v2112, v2206, v2212, v2306, v2312
+| align="center" | 8, 9, 10, 11, v2006, v2012, v2112, v2206, v2212, v2306, v2312
 | Documentation: [[OpenFOAM]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. Homepage: https://www.openfoam.com/ URL: https://www.openfoam.com/ Keyword:phys<br /><br /><br /></div>
 |-
@@ Line 3,637: / Line 3,092: @@
 | align="center" | [https://openimageio.org/ openimageio]
 | align="center" | vis
-| align="center" | 1.8.15, 2.1.17.0, 2.4.7.1, 2.4.14.0
+| align="center" | 2.1.17.0, 2.4.7.1, 2.4.14.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, and applications. Homepage: https://openimageio.org/ URL: https://openimageio.org/ Compatible modules: python/3.10, python/3.11 Keyword:vis<br /><br /><br /></div>
 |-
@@ Line 3,647: / Line 3,102: @@
 | align="center" | [http://openmm.org openmm]
 | align="center" | chem
-| align="center" | 7.1.1, 7.4.1, 7.5.0, 7.6.0, 7.7.0, 8.0.0
+| align="center" | 7.5.0, 7.6.0, 7.7.0, 8.0.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMM is a toolkit for molecular simulation. Homepage: http://openmm.org URL: http://openmm.org Compatible modules: python/3.10, python/3.11 Extensions: pdbfixer-1.8.1 Keyword:chem<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMM is a toolkit for molecular simulation. Homepage: http://openmm.org URL: http://openmm.org Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: pdbfixer-1.8.1 Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [http://openmm.org openmm-alphafold]
@@ Line 3,662: / Line 3,117: @@
 | align="center" | [https://gitlab.com/Molcas/OpenMolcas openmolcas]
 | align="center" | chem
-| align="center" | 18.9, 20.07, 20.10
+| align="center" | 20.10
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMolcas is a quantum chemistry software package Homepage: https://gitlab.com/Molcas/OpenMolcas URL: https://gitlab.com/Molcas/OpenMolcas Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://www.open-mpi.org/ openmpi]
 | align="center" | mpi
-| align="center" | 1.8.8, 1.10.7, 2.1.1, 3.1.2, 3.1.4, 4.0.1, 4.0.3, 4.0.5, 4.1.1, 4.1.4, 4.1.5, 5.0.3
+| align="center" | 4.0.3, 4.0.5, 4.1.1, 4.1.4, 4.1.5, 5.0.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Open MPI Project is an open source MPI-3 implementation. Homepage: https://www.open-mpi.org/ URL: https://www.open-mpi.org/ Keyword:mpi<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/OpenMS/OpenMS openms]
-| align="center" | -
-| align="center" | 2.5.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software. Homepage: https://github.com/OpenMS/OpenMS URL: https://github.com/OpenMS/OpenMS<br /><br /><br /></div>
 |-
 | align="center" | [http://www.openmx-square.org/ openmx]
 | align="center" | chem
-| align="center" | 3.8, 3.9, 3.9.9
+| align="center" | 3.9, 3.9.9
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials, and pseudo-atomic localized basis functions. The methods and algorithms used in OpenMX and their implementation are carefully designed for the realization of large-scale ab initio electronic structure calculations on parallel computers based on the MPI or MPI/OpenMP hybrid parallelism. Homepage: http://www.openmx-square.org/ URL: http://www.openmx-square.org/ Keyword:chem<br /><br /><br /></div>
 |-
-| align="center" | [http://code.google.com/p/openpgm/ openpgm]
+| align="center" | [https://code.google.com/p/openpgm/ openpgm]
 | align="center" | tools
 | align="center" | 5.2.122
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility. Homepage: http://code.google.com/p/openpgm/ Keyword:tools<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility. Homepage: https://code.google.com/p/openpgm/ URL: https://code.google.com/p/openpgm/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/OpenRefine/OpenRefine openrefine]
 | align="center" | -
-| align="center" | 3.3, 3.4.1
+| align="center" | 3.4.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenRefine is a power tool that allows you to load data, understand it, clean it up, reconcile it, and augment it with data coming from the web. Homepage: https://github.com/OpenRefine/OpenRefine URL: https://github.com/OpenRefine/OpenRefine<br /><br /><br /></div>
 |-
 | align="center" | [http://opensees.berkeley.edu/ opensees]
 | align="center" | -
-| align="center" | 3.1.0, 3.2.0, 3.5.0
+| align="center" | 3.2.0, 3.5.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenSees is a software framework for developing applications to simulate the performance of structural and geotechnical systems subjected to earthquakes. This version is built using DISTRIBUTED_MP platform setting. Homepage: http://opensees.berkeley.edu/ URL: http://opensees.berkeley.edu/<br /><br /><br /></div>
 |-
@@ Line 3,713: / Line 3,163: @@
 | align="center" | -
 | align="center" | 0.10.0, 1.3.1, 1.3.2
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Open Volume Kernel Library (Intel Open VKL) is a collection of high-performance volume computation kernels, developed at Intel. The target users of Open VKL are graphics application engineers who want to improve the performance of their volume rendering applications by leveraging Open VKLs performance-optimized kernels, which include volume traversal and sampling functionality for a variety of volumetric data formats. The kernels are optimized for the latest Intel processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Homepage: https://github.com/OpenVKL/openvkl URL: https://github.com/OpenVKL/openvkl<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Open Volume Kernel Library (Intel Open VKL) is a collection of high-performance volume computation kernels, developed at Intel. The target users of Open VKL are graphics application engineers who want to improve the performance of their volume rendering applications by leveraging Open VKL's performance-optimized kernels, which include volume traversal and sampling functionality for a variety of volumetric data formats. The kernels are optimized for the latest Intel processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Homepage: https://github.com/OpenVKL/openvkl URL: https://github.com/OpenVKL/openvkl<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/CSB5/OPERA-MS opera-ms]
@@ Line 3,723: / Line 3,173: @@
 | align="center" | -
 | align="center" | 6.5.0, 7.7.0, 8.0.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OptiX is NVIDIA SDK for easy ray tracing performance. It provides a simple framework for accessing the GPUs massive ray tracing power using state-of-the-art GPU algorithms. Homepage: https://developer.nvidia.com/optix URL: https://developer.nvidia.com/optix<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OptiX is NVIDIA SDK for easy ray tracing performance. It provides a simple framework for accessing the GPU's massive ray tracing power using state-of-the-art GPU algorithms. Homepage: https://developer.nvidia.com/optix URL: https://developer.nvidia.com/optix<br /><br /><br /></div>
 |-
 | align="center" | [https://support.illumina.com/downloads/dragen_decompression_software_v261_software-linux.html orad]
@@ Line 3,732: / Line 3,182: @@
 | align="center" | [http://cec.mpg.de/forum/ orca]
 | align="center" | chem
-| align="center" | 4.1.2, 4.2.0, 4.2.1, 5.0.1, 5.0.2, 5.0.3, 5.0.4
+| align="center" | 4.2.1, 5.0.1, 5.0.2, 5.0.3, 5.0.4
 | Documentation: [[ORCA]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. Homepage: http://cec.mpg.de/forum/ URL: http://cec.mpg.de/forum/ Keyword:chem<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/wwood/OrfM orfm]
-| align="center" | -
-| align="center" | 0.7.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A simple and not slow open reading frame (ORF) caller. No bells or whistles like frameshift detection, just a straightforward goal of returning a FASTA file of open reading frames over a certain length from a FASTA/Q file of nucleotide sequences. Homepage: https://github.com/wwood/OrfM<br /><br /><br /></div>
 |-
 | align="center" | [http://orthomcl.org/ orthomcl]
 | align="center" | bio
 | align="center" | 2.0.9
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. Homepage: http://orthomcl.org/ Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. Homepage: http://orthomcl.org/ URL: http://orthomcl.org/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/ospray/ospray ospray]
@@ Line 3,757: / Line 3,202: @@
 | align="center" | [https://mvapich.cse.ohio-state.edu/benchmarks/ osu-micro-benchmarks]
 | align="center" | tools
-| align="center" | 5.3.2, 5.6.1, 5.6.2, 5.6.3, 5.9, 7.1-1, 7.2
+| align="center" | 5.6.2, 5.6.3, 5.9, 7.1-1, 7.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OSU Micro-Benchmarks Homepage: https://mvapich.cse.ohio-state.edu/benchmarks/ URL: https://mvapich.cse.ohio-state.edu/benchmarks/ Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 3,772: / Line 3,217: @@
 | align="center" | [http://www.p4est.org/ p4est]
 | align="center" | math
-| align="center" | 1.1, 2.0, 2.2, 2.3.2, 2.8.5
+| align="center" | 2.2, 2.3.2, 2.8.5
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The p4est software library enables the dynamic management of a collection of adaptive octrees, conveniently called a forest of octrees. p4est is designed to work in parallel and scales to hundreds of thousands of processor cores. It is free software released under GNU General Public Licence version 2, or (at your option) any later version. Homepage: http://www.p4est.org/ URL: http://www.p4est.org/ Keyword:math<br /><br /><br /></div>
-|-
-| align="center" | [http://www.p4vasp.at p4vasp]
-| align="center" | chem
-| align="center" | 0.3.30
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: p4vasp is the VASP Visualization Tool that can be used to display structure, unitcell, supercell, charge/probability/spin density, local potential, forces, velocities, dynamics, measure distances and angles, .... It can be used also to analyze electronic properties, total and local DOS and band structure Homepage: http://www.p4vasp.at Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [http://m3g.iqm.unicamp.br/packmol packmol]
 | align="center" | chem
-| align="center" | 18.013, 20.3.3
+| align="center" | 20.3.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Packing Optimization for Molecular Dynamics Simulations Homepage: http://m3g.iqm.unicamp.br/packmol URL: http://m3g.iqm.unicamp.br/packmol Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 3,789: / Line 3,229: @@
 | align="center" | 2.18.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: pagmo is a C++ scientific library for massively parallel optimization. Homepage: https://esa.github.io/pagmo2 URL: https://esa.github.io/pagmo2<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/Population-Transcriptomics/pairedBamToBed12 pairedbamtobed12]
-| align="center" | -
-| align="center" | 1.2
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: pairedBamToBed12 converts properly paired BAM alignments to BED12 format. Typical proper pairs will be represented by a 2 blocks BED12 entry. Additional blocks are produced when an alignment contains long deletion (CIGAR N-op). Thickness indicates the first read of the pair. The BAM input file must be grouped/sorted by query name (not alignment position). Homepage: https://github.com/Population-Transcriptomics/pairedBamToBed12 URL: https://github.com/Population-Transcriptomics/pairedBamToBed12<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/4dn-dcic/pairix pairix]
@@ Line 3,802: / Line 3,237: @@
 | align="center" | [http://abacus.gene.ucl.ac.uk/software/paml.html paml]
 | align="center" | bio
-| align="center" | 4.9h, 4.9j, 4.10.7
+| align="center" | 4.9j, 4.10.7
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html URL: http://abacus.gene.ucl.ac.uk/software/paml.html Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [https://www.cbcb.umd.edu/software/panarray panarray]
-| align="center" | -
-| align="center" | 1.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PanArray is an oligonucleotide probe selection algorithm for tiling multiple genome sequences using a minimal number of probes. It is capable of fully tiling all genomes of a species on a single microarray chip. These unique pan-genome tiling arrays provide maximum flexibility for the analysis of both known and uncharacterized strains. Homepage: https://www.cbcb.umd.edu/software/panarray<br /><br /><br /></div>
 |-
 | align="center" | [https://www.google.ca/search?q=panther panther]
@@ Line 3,817: / Line 3,247: @@
 | align="center" | [https://icl.cs.utk.edu/projects/papi/ papi]
 | align="center" | tools
-| align="center" | 5.6.0, 6.0.0
+| align="center" | 6.0.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack. Homepage: https://icl.cs.utk.edu/projects/papi/ URL: https://icl.cs.utk.edu/projects/papi/ Keyword:tools<br /><br /><br /></div>
 |-
-| align="center" | [https://developer.nvidia.com/nvidia-parabricks parabricks]
+| align="center" | [https://github.com/NCAR/ParallelIO parallelio]
-| align="center" | -
-| align="center" | 2.5.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Analyzing genomic data is computationally intensive. Time and cost are significant barriers to using genomics data for precision medicine. The NVIDIA Parabricks Genomics Analysis Toolkit breaks down those barriers, providing GPU-accelerated genomic analysis. Data that once took days to analyze can now be done in under an hour. Homepage: https://developer.nvidia.com/nvidia-parabricks URL: https://developer.nvidia.com/nvidia-parabricks<br /><br /><br /></div>
-|-
-| align="center" | [http://savannah.gnu.org/projects/parallel/ parallel]
-| align="center" | tools
-| align="center" | 20160722
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: parallel: Build and execute shell commands in parallel Homepage: http://savannah.gnu.org/projects/parallel/ Keyword:tools<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/NCAR/ParallelIO parallelio]
 | align="center" | -
 | align="center" | 2.5.4
@@ Line 3,842: / Line 3,262: @@
 | align="center" | [https://www.paraview.org paraview]
 | align="center" | vis
-| align="center" | 5.5.2, 5.8.0, 5.9.1, 5.10.0, 5.11.0, 5.11.2
+| align="center" | 5.8.0, 5.9.1, 5.10.0, 5.11.0, 5.11.2
 | Documentation: [[Visualization]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ParaView is a scientific parallel visualizer. Homepage: https://www.paraview.org URL: https://www.paraview.org Compatible modules: python/3.10, python/3.11 Keyword:vis<br /><br /><br /></div>
 |-
 | align="center" | [https://www.paraview.org paraview-offscreen]
 | align="center" | vis
-| align="center" | 5.5.2, 5.8.0, 5.9.1, 5.10.0, 5.11.0
+| align="center" | 5.8.0, 5.9.1, 5.10.0, 5.11.0
 | Documentation: [[Visualization]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ParaView is a scientific parallel visualizer. Homepage: https://www.paraview.org URL: https://www.paraview.org Compatible modules: python/3.8, python/3.9, python/3.10 Keyword:vis<br /><br /><br /></div>
 |-
@@ Line 3,863: / Line 3,283: @@
 | align="center" | math
 | align="center" | 4.0.3
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. Homepage: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview Keyword:math<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. Homepage: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview URL: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [http://www-users.cs.umn.edu/~moulitsa/software.html parmgridgen]
@@ Line 3,877: / Line 3,297: @@
 | align="center" | [http://pbbam.readthedocs.io/ pbbam]
 | align="center" | bio
-| align="center" | 1.0.7, 1.7.0, 20170508
+| align="center" | 1.0.7, 1.7.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The pbbam software package provides components to create, query, and edit PacBio BAM files and associated indices. Homepage: http://pbbam.readthedocs.io/ Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The pbbam software package provides components to create, query, and edit PacBio BAM files and associated indices. Homepage: http://pbbam.readthedocs.io/ URL: http://pbbam.readthedocs.io/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/PacificBiosciences/pbcopper pbcopper]
@@ Line 3,884: / Line 3,304: @@
 | align="center" | 1.4.0, 1.9.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The pbcopper library provides a suite of data structures, algorithms, and utilities for C++ applications. Homepage: https://github.com/PacificBiosciences/pbcopper URL: https://github.com/PacificBiosciences/pbcopper<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/PacificBiosciences/pbdagcon pbdagcon]
-| align="center" | bio
-| align="center" | 20170330
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus) which is a sequence consensus algorithm based on using directed acyclic graphs to encode multiple sequence alignment. Homepage: https://github.com/PacificBiosciences/pbdagcon Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/PacificBiosciences/pbmm2 pbmm2]
@@ Line 3,899: / Line 3,314: @@
 | align="center" | 15.8.24
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. Homepage: https://sourceforge.net/p/pb-jelly/wiki/Home/ URL: https://sourceforge.net/p/pb-jelly/wiki/Home/ Extensions: networkx-1.10 Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [https://pcmsolver.readthedocs.org pcmsolver]
-| align="center" | chem
-| align="center" | 1.2.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An API for the Polarizable Continuum Model. Homepage: https://pcmsolver.readthedocs.org Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://www.pcre.org/ pcre]
 | align="center" | -
-| align="center" | 8.39, 8.44
+| align="center" | 8.44
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. Homepage: https://www.pcre.org/ URL: https://www.pcre.org/<br /><br /><br /></div>
 |-
 | align="center" | [https://www.pcre.org/ pcre2]
 | align="center" | -
-| align="center" | 10.31, 10.34
+| align="center" | 10.34
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. Homepage: https://www.pcre.org/ URL: https://www.pcre.org/<br /><br /><br /></div>
 |-
@@ Line 3,922: / Line 3,332: @@
 | align="center" | [https://www.cs.uoregon.edu/research/pdt/ pdt]
 | align="center" | -
-| align="center" | 3.25, 3.25.1
+| align="center" | 3.25.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations. Homepage: https://www.cs.uoregon.edu/research/pdt/ URL: https://www.cs.uoregon.edu/research/pdt/<br /><br /><br /></div>
 |-
 | align="center" | [https://cme.h-its.org/exelixis/web/software/pear/ pear]
 | align="center" | bio
-| align="center" | 0.9.10, 0.9.11
+| align="center" | 0.9.11
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. Homepage: https://cme.h-its.org/exelixis/web/software/pear/ URL: https://cme.h-its.org/exelixis/web/software/pear/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://penncnv.openbioinformatics.org/ penncnv]
 | align="center" | bio
-| align="center" | 1.0.4, 1.0.5
+| align="center" | 1.0.5
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. Homepage: https://penncnv.openbioinformatics.org/ URL: https://penncnv.openbioinformatics.org/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/percolator percolator]
 | align="center" | bio
-| align="center" | 3-02, 3.06
+| align="center" | 3.06
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Semi-supervised learning for peptide identification from shotgun proteomics datasets Homepage: https://github.com/percolator URL: https://github.com/percolator Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://www.perl.org/ perl]
 | align="center" | tools
-| align="center" | 5.16.3, 5.22.2, 5.22.4, 5.30.2, 5.36.1
+| align="center" | 5.30.2, 5.36.1
-| Documentation: [[Perl]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Larry Wall's Practical Extraction and Report Language Includes a small selection of extra CPAN packages for core functionality. Homepage: https://www.perl.org/ URL: https://www.perl.org/ Extensions: Algorithm::Dependency-1.112, Algorithm::Diff-1.201, aliased-0.34, AnyEvent-7.17, App::Cmd-0.335, App::cpanminus-1.7046, AppConfig-1.71, Archive::Extract-0.88, Array::Transpose-0.06, Array::Utils-0.5, Authen::NTLM-1.09, Authen::SASL-2.16, AutoLoader-5.74, B::COW-0.007, B::Hooks::EndOfScope-0.26, B::Lint-1.20, boolean-0.46, Business::ISBN-3.008, Business::ISBN::Data-20230516.001, Canary::Stability-2013, Capture::Tiny-0.48, Carp-1.50, Carp::Clan-6.08, Carp::Heavy-1.50, CGI-4.57, Class::Accessor-0.51, Class::Data::Inheritable-0.09, Class::DBI-v3.0.17, Class::DBI::SQLite-0.11, Class::Inspector-1.36, Class::ISA-0.36, Class::Load-0.25, Class::Load::XS-0.10, Class::Method::Modifiers-2.15, Class::Singleton-1.6, Class::Tiny-1.008, Class::Trigger-0.15, Class::XSAccessor-1.19, Clone-0.46, Clone::Choose-0.010, common::sense-3.75, Compress::Raw::Zlib-2.204, Config::General-2.65, Config::INI-0.029, Config::MVP-2.200013, Config::MVP::Reader::INI-2.101465, Config::Simple-4.58, Config::Tiny-2.29, Const::Exporter-1.2.2, Const::Fast-0.014, constant-1.33, CPAN::Meta::Check-0.017, CPAN::Uploader-0.103018, CPANPLUS-0.9914, Crypt::DES-2.07, Crypt::Rijndael-1.16, Cwd-3.75, Cwd::Guard-0.05, Data::Dump-1.25, Data::Dumper-2.183, Data::Dumper::Concise-2.023, Data::Grove-0.08, Data::OptList-0.114, Data::Section-0.200008, Data::Section::Simple-0.07, Data::Stag-0.14, Data::Types-0.17, Data::UUID-1.226, Date::Handler-1.2, Date::Language-2.33, DateTime-1.59, DateTime::Locale-1.38, DateTime::TimeZone-2.60, DateTime::Tiny-1.07, DBD::CSV-0.60, DBD::SQLite-1.72, DBI-1.643, DBIx::Admin::CreateTable-2.11, DBIx::Admin::DSNManager-2.02, DBIx::Admin::TableInfo-3.04, DBIx::ContextualFetch-1.03, DBIx::Simple-1.37, Devel::CheckCompiler-0.07, Devel::CheckLib-1.16, Devel::Cycle-1.12, Devel::FindPerl-0.016, Devel::GlobalDestruction-0.14, Devel::OverloadInfo-0.007, Devel::Size-0.83, Devel::StackTrace-2.04, Digest::HMAC-1.04, Digest::MD5::File-0.08, Digest::SHA1-2.13, Dist::CheckConflicts-0.11, Dist::Zilla-6.030, Email::Date::Format-1.008, Encode-3.19, Encode::Locale-1.05, Error-0.17029, Eval::Closure-0.14, Exception::Class-1.45, Expect-1.35, Exporter-5.77, Exporter::Declare-0.114, Exporter::Tiny-1.006002, ExtUtils::CBuilder-0.280236, ExtUtils::Config-0.008, ExtUtils::Constant-0.25, ExtUtils::CppGuess-0.26, ExtUtils::Helpers-0.026, ExtUtils::InstallPaths-0.012, ExtUtils::MakeMaker-7.70, ExtUtils::ParseXS-3.44, Fennec::Lite-0.004, File::CheckTree-4.42, File::Copy::Recursive-0.45, File::Copy::Recursive::Reduced-0.006, File::Find::Rule-0.34, File::Find::Rule::Perl-1.16, File::Grep-0.02, File::HomeDir-1.006, File::Listing-6.15, File::Next-1.18, File::Path-2.18, File::pushd-1.016, File::Remove-1.61, File::ShareDir-1.118, File::ShareDir::Install-0.14, File::Slurp-9999.32, File::Slurp::Tiny-0.004, File::Slurper-0.014, File::Spec-3.75, File::Temp-0.2311, File::Which-1.27, Font::TTF-1.06, Getopt::Long-2.54, Getopt::Long::Descriptive-0.111, Git-0.42, GO-0.04, GO::Utils-0.15, Graph-0.9726, Graph::ReadWrite-2.10, Hash::Merge-0.302, Hash::Objectify-0.008, Heap-0.80, Hook::LexWrap-0.26, HTML::Entities::Interpolate-1.10, HTML::Form-6.11, HTML::Parser-3.81, HTML::Tagset-3.20, HTML::Template-2.97, HTML::Tree-5.07, HTTP::CookieJar-0.014, HTTP::Cookies-6.10, HTTP::Daemon-6.16, HTTP::Date-6.05, HTTP::Message-6.44, HTTP::Negotiate-6.01, HTTP::Tiny-0.082, if-0.0608, Ima::DBI-0.35, Import::Into-1.002005, Importer-0.026, Inline-0.86, IO::Compress::Zip-2.204, IO::File-1.51, IO::HTML-1.004, IO::Socket::SSL-2.083, IO::String-1.08, IO::Stringy-2.113, IO::TieCombine-1.005, IO::Tty-1.17, IO::Tty-1.17, IPC::Cmd-1.04, IPC::Run-20220807.0, IPC::Run3-0.048, IPC::System::Simple-1.30, JSON-4.10, JSON::MaybeXS-1.004005, JSON::XS-4.03, Lingua::EN::PluralToSingular-0.21, List::AllUtils-0.19, List::MoreUtils-0.430, List::MoreUtils::XS-0.430, List::SomeUtils-0.59, List::UtilsBy-0.12, local::lib-2.000029, Locale::Maketext::Simple-0.21, Log::Dispatch-2.71, Log::Dispatch::Array-1.005, Log::Dispatchouli-3.002, Log::Handler-0.90, Log::Log4perl-1.57, Log::Message-0.08, Log::Message::Simple-0.10, Log::Report-1.34, Log::Report::Optional-1.07, Logger::Simple-2.0, LWP::MediaTypes-6.04, LWP::Protocol::https-6.10, LWP::Simple-6.70, Mail::Util-2.21, Math::Bezier-0.01, Math::CDF-0.1, Math::Round-0.07, Math::Utils-1.14, Math::VecStat-0.08, MCE::Mutex-1.884, Meta::Builder-0.004, MIME::Base64-3.16, MIME::Charset-v1.013.1, MIME::Lite-3.033, MIME::Types-2.24, Mixin::Linewise::Readers-0.111, Mock::Quick-1.111, Module::Build-0.4234, Module::Build::Tiny-0.045, Module::Build::XSUtil-0.19, Module::CoreList-5.20230423, Module::Implementation-0.09, Module::Install-1.21, Module::Load-0.36, Module::Load::Conditional-0.74, Module::Metadata-1.000038, Module::Path-0.19, Module::Path-0.19, Module::Pluggable-5.2, Module::Runtime-0.016, Module::Runtime::Conflicts-0.003, Moo-2.005005, Moose-2.2203, MooseX::LazyRequire-0.11, MooseX::OneArgNew-0.007, MooseX::Role::Parameterized-1.11, MooseX::SetOnce-0.203, MooseX::Types-0.50, MooseX::Types::Perl-0.101344, Mouse-v2.5.10, Mozilla::CA-20221114, MRO::Compat-0.15, namespace::autoclean-0.29, namespace::clean-0.27, Net::Domain-3.15, Net::HTTP-6.22, Net::SMTP::SSL-1.04, Net::SNMP-v6.0.1, Net::SSLeay-1.92, Number::Compare-0.03, Number::Format-1.75, Object::Accessor-0.48, Object::InsideOut-4.05, Object::InsideOut-4.05, Package::Constants-0.06, Package::DeprecationManager-0.18, Package::Stash-0.40, Package::Stash::XS-0.30, PadWalker-2.5, Parallel::ForkManager-2.02, Params::Check-0.38, Params::Util-1.102, Params::Validate-1.31, Params::ValidationCompiler-0.31, parent-0.241, Parse::RecDescent-1.967015, Parse::Yapp-1.21, Path::Tiny-0.144, PDF::API2-2.044, Perl::OSType-1.010, Perl::PrereqScanner-1.100, PerlIO::utf8_strict-0.010, Pod::Elemental-0.103006, Pod::Escapes-1.07, Pod::Eventual-0.094003, Pod::LaTeX-0.61, Pod::Man-5.01, Pod::Parser-1.66, Pod::Plainer-1.04, Pod::POM-2.01, Pod::Simple-3.45, Pod::Weaver-4.019, PPI-1.276, Readonly-2.05, Ref::Util-0.204, Regexp::Common-2017060201, Role::HasMessage-0.007, Role::Identifiable::HasIdent-0.009, Role::Tiny-2.002004, Scalar::Util-1.63, Scalar::Util::Numeric-0.40, Scope::Guard-0.21, Set::Array-0.30, Set::IntervalTree-0.12, Set::IntSpan-1.19, Set::IntSpan::Fast-1.15, Set::Object-1.42, Set::Scalar-1.29, Shell-0.73, Socket-2.036, Software::License-0.104003, Specio-0.48, Spiffy-0.46, SQL::Abstract-2.000001, SQL::Statement-1.414, Statistics::Basic-1.6611, Statistics::Descriptive-3.0800, Storable-3.25, strictures-2.000006, String::Errf-0.009, String::Flogger-1.101246, String::Formatter-1.235, String::Print-0.94, String::RewritePrefix-0.009, String::Truncate-1.100603, String::TtyLength-0.03, Sub::Exporter-0.989, Sub::Exporter::ForMethods-0.100055, Sub::Exporter::GlobExporter-0.006, Sub::Exporter::Progressive-0.001013, Sub::Identify-0.14, Sub::Info-0.002, Sub::Install-0.929, Sub::Name-0.27, Sub::Quote-2.006008, Sub::Uplevel-0.2800, SVG-2.87, Switch-2.17, Sys::Info-0.7811, Sys::Info::Base-0.7807, Sys::Info::Driver::Linux-0.7905, Sys::Info::Driver::Linux::Device::CPU-0.7905, Sys::Info::Driver::Unknown-0.79, Sys::Info::Driver::Unknown::Device::CPU-0.79, Template-3.101, Template::Plugin::Number::Format-1.06, Term::Encoding-0.03, Term::ReadKey-2.38, Term::ReadLine::Gnu-1.45, Term::Table-0.016, Term::UI-0.50, Test-1.26, Test2::Plugin::NoWarnings-0.09, Test2::Require::Module-0.000155, Test::Base-0.89, Test::CheckDeps-0.010, Test::ClassAPI-1.07, Test::CleanNamespaces-0.24, Test::Deep-1.204, Test::Differences-0.69, Test::Exception-0.43, Test::FailWarnings-0.008, Test::Fatal-0.017, Test::File-1.993, Test::File::ShareDir::Dist-1.001002, Test::Harness-3.44, Test::LeakTrace-0.17, Test::Memory::Cycle-1.06, Test::More::UTF8-0.05, Test::Most-0.38, Test::Needs-0.002010, Test::NoWarnings-1.06, Test::Object-0.08, Test::Output-1.033, Test::Pod-1.52, Test::Requires-0.11, Test::RequiresInternet-0.05, Test::Simple-1.302195, Test::SubCalls-1.10, Test::Sys::Info-0.23, Test::Version-2.09, Test::Warn-0.37, Test::Warnings-0.031, Test::Without::Module-0.21, Test::YAML-1.07, Text::Aligner-0.16, Text::Balanced-2.06, Text::CSV-2.02, Text::CSV_XS-1.50, Text::Diff-1.45, Text::Format-0.62, Text::Glob-0.11, Text::Iconv-1.7, Text::ParseWords-3.31, Text::Soundex-3.05, Text::Table-1.135, Text::Table::Manifold-1.03, Text::Template-1.61, Thread::Queue-3.13, threads-2.21, Throwable-1.001, Tie::Function-0.02, Tie::IxHash-1.23, Time::HiRes-1.9764, Time::Local-1.35, Time::Piece-1.3401, Time::Piece::MySQL-0.06, Tree::DAG_Node-1.32, Try::Tiny-0.31, Type::Tiny-2.004000, Types::Serialiser-1.01, Types::Serialiser-1.01, Unicode::EastAsianWidth-12.0, Unicode::LineBreak-2019.001, UNIVERSAL::moniker-0.08, Unix::Processors-2.046, Unix::Processors-2.046, URI-5.19, Variable::Magic-0.63, version-0.9929, Want-0.29, WWW::RobotRules-6.02, XML::Bare-0.53, XML::DOM-1.46, XML::Filter::BufferText-1.01, XML::NamespaceSupport-1.12, XML::Parser-2.46, XML::RegExp-0.04, XML::SAX-1.02, XML::SAX::Base-1.09, XML::SAX::Expat-0.51, XML::SAX::Writer-0.57, XML::Simple-2.25, XML::Tiny-2.07, XML::Twig-3.52, XML::Writer-0.900, XML::XPath-1.48, XSLoader-0.24, YAML-1.30, YAML::Tiny-1.74 Keyword:tools<br /><br /><br /></div>
+| Documentation: [[Perl]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Larry Wall's Practical Extraction and Report Language Includes a small selection of extra CPAN packages for core functionality. Homepage: https://www.perl.org/ URL: https://www.perl.org/ Extensions: Carp-1.50, constant-1.33, Data::Dumper-2.183, Exporter-5.77, File::Path-2.18, File::Spec-3.75, Getopt::Long-2.54, IO::File-1.51, Text::ParseWords-3.31, Thread::Queue-3.13, threads-2.21 Keyword:tools<br /><br /><br /></div>
-|-
-| align="center" | [https://metacpan.org/pod/Perl4::CoreLibs perl4-corelibs]
-| align="center" | tools
-| align="center" | 0.003
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Libraries historically supplied with Perl 4 Homepage: https://metacpan.org/pod/Perl4::CoreLibs Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [http://www.mcs.anl.gov/petsc petsc]
 | align="center" | tools
-| align="center" | 3.7.5, 3.10.2, 3.10.5, 3.11.3, 3.12.0, 3.12.4, 3.13.3, 3.13.6, 3.14.1, 3.15.0, 3.17.1, 3.19.2, 3.20.0
+| align="center" | 3.12.4, 3.13.3, 3.13.6, 3.14.1, 3.15.0, 3.17.1, 3.19.2, 3.20.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Homepage: http://www.mcs.anl.gov/petsc URL: http://www.mcs.anl.gov/petsc Compatible modules: python/3.10, python/3.11 Extensions: petsc4py-3.20.0 Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [http://www.mcs.anl.gov/petsc petsc-64bits]
 | align="center" | tools
-| align="center" | 3.10.2, 3.17.1, 3.19.2
+| align="center" | 3.17.1, 3.19.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Homepage: http://www.mcs.anl.gov/petsc URL: http://www.mcs.anl.gov/petsc Compatible modules: python/3.9, python/3.10, python/3.11 Extensions: petsc4py-3.19.2 Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [http://www.mcs.anl.gov/petsc petsc-complex]
 | align="center" | tools
-| align="center" | 3.10.2, 3.11.3, 3.20.0
+| align="center" | 3.20.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Homepage: http://www.mcs.anl.gov/petsc URL: http://www.mcs.anl.gov/petsc Compatible modules: python/3.10, python/3.11 Extensions: petsc4py-3.20.0 Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 3,994: / Line 3,399: @@
 | align="center" | 3.2.12
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A suite of tools to build and search generalized profiles (protein and DNA). Homepage: https://github.com/sib-swiss/pftools3 URL: https://github.com/sib-swiss/pftools3<br /><br /><br /></div>
-|-
-| align="center" | [http://www.pgroup.com/ pgi]
-| align="center" | tools
-| align="center" | 13.10, 16.9, 17.3, 19.4
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C, C++ and Fortran compilers from The Portland Group - PGI Homepage: http://www.pgroup.com/ URL: http://www.pgroup.com/<br /><br /><br /></div>
 |-
 | align="center" | [http://www.astro.caltech.edu/~tjp/pgplot/ pgplot]
@@ Line 4,022: / Line 3,422: @@
 | align="center" | [http://evolution.genetics.washington.edu/phylip phylip]
 | align="center" | bio
-| align="center" | 3.697, 3.698
+| align="center" | 3.698
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PHYLIP is a free package of programs for inferring phylogenies. Homepage: http://evolution.genetics.washington.edu/phylip URL: http://evolution.genetics.washington.edu/phylip Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 4,047: / Line 3,447: @@
 | align="center" | [https://github.com/FePhyFoFum/phyx phyx]
 | align="center" | bio
-| align="center" | 0.999, 1.1
+| align="center" | 1.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: phyx performs phylogenetics analyses on trees and sequences. Homepage: https://github.com/FePhyFoFum/phyx URL: https://github.com/FePhyFoFum/phyx Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://broadinstitute.github.io/picard/ picard]
 | align="center" | bio
-| align="center" | 2.1.1, 2.10.7, 2.17.3, 2.18.9, 2.20.6, 2.23.2, 2.23.3, 2.26.3, 3.1.0
+| align="center" | 2.23.3, 2.26.3, 3.1.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A set of tools (in Java) for working with next generation sequencing data in the BAM format. Homepage: https://broadinstitute.github.io/picard/ URL: https://broadinstitute.github.io/picard/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 4,062: / Line 3,462: @@
 | align="center" | [https://github.com/broadinstitute/pilon pilon]
 | align="center" | bio
-| align="center" | 1.22, 1.23, 1.24
+| align="center" | 1.23, 1.24
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Pilon is an automated genome assembly improvement and variant detection tool Homepage: https://github.com/broadinstitute/pilon URL: https://github.com/broadinstitute/pilon Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 4,069: / Line 3,469: @@
 | align="center" | 0.2.5b9-20170508
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads. Homepage: http://gmt.genome.wustl.edu/packages/pindel/ URL: http://gmt.genome.wustl.edu/packages/pindel/ Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://www.irisa.fr/symbiose/projects/plast/ plast]
-| align="center" | bio
-| align="center" | 2.3.2
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PLAST is a parallel alignment search tool for comparing large protein banks Homepage: http://www.irisa.fr/symbiose/projects/plast/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://platanus.bio.titech.ac.jp/ platanus]
@@ Line 4,085: / Line 3,480: @@
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Platanus-allee is an assembler derived from Platanus assembler, however, it was developed with another concept. Platanus-allee tries to construct each haplotype sequence from the beginning and pair them as homologous chromosomes, while Platanus constructs consensus sequence of homologous chromosomes at first and tries to split into each haplotype sequence. Therefore, Platanus-allee marks better performance for highly heterozygous species genome or highly diverged genomic regions. Homepage: http://platanus.bio.titech.ac.jp/ URL: http://platanus.bio.titech.ac.jp/<br /><br /><br /></div>
 |-
-| align="center" | [http://www.well.ox.ac.uk/platypus platypus]
+| align="center" | [https://www.cog-genomics.org/plink/2.0/ plink]
-| align="center" | bio
-| align="center" | 0.8.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. Homepage: http://www.well.ox.ac.uk/platypus Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://pngu.mgh.harvard.edu/~purcell/plink/ plink]
 | align="center" | bio
-| align="center" | 1.9b_4.1-x86_64, 1.9b_5.2-x86_64, 1.9b_6.21-x86_64, 2.00a2.3_x86_64, 2.00a3.6, 2.00a5.8, 2.00-10252019-avx2, 2.00-20231024-avx2, 1.07
+| align="center" | 2.00a3.6, 2.00-20231024-avx2, 2.00a5.8, 1.9b_6.21-x86_64, 2.00-10252019-avx2
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results. Homepage: http://pngu.mgh.harvard.edu/~purcell/plink/ Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Whole-genome association analysis toolset Homepage: https://www.cog-genomics.org/plink/2.0/ URL: https://www.cog-genomics.org/plink/2.0/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://plplot.sourceforge.net plplot]
@@ Line 4,102: / Line 3,492: @@
 | align="center" | [https://www.plumed.org plumed]
 | align="center" | chem
-| align="center" | 2.3.7, 2.4.2, 2.4.3, 2.5.2, 2.5.3, 2.5.4, 2.6.1, 2.6.2, 2.7.0, 2.7.1, 2.7.2, 2.7.3, 2.7.4, 2.7.6, 2.8.1, 2.8.3, 2.9.0
+| align="center" | 2.6.1, 2.6.2, 2.7.0, 2.7.1, 2.7.2, 2.7.3, 2.7.4, 2.7.6, 2.8.1, 2.8.3, 2.9.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. Homepage: https://www.plumed.org URL: https://www.plumed.org Compatible modules: python/3.10, python/3.11 Extensions: plumed-2.9.0 Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 4,112: / Line 3,502: @@
 | align="center" | [https://pmix.org/ pmix]
 | align="center" | -
-| align="center" | 1.2.5, 3.1.5, 3.2.3, 4.1.2, 4.2.4, 5.0.2
+| align="center" | 3.1.5, 3.2.3, 4.1.2, 4.2.4, 5.0.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Process Management for Exascale Environments PMI Exascale (PMIx) represents an attempt to provide an extended version of the PMI standard specifically designed to support clusters up to and including exascale sizes. The overall objective of the project is not to branch the existing pseudo-standard definitions - in fact, PMIx fully supports both of the existing PMI-1 and PMI-2 APIs - but rather to (a) augment and extend those APIs to eliminate some current restrictions that impact scalability, and (b) provide a reference implementation of the PMI-server that demonstrates the desired level of scalability. Homepage: https://pmix.org/ URL: https://pmix.org/<br /><br /><br /></div>
 |-
@@ Line 4,137: / Line 3,527: @@
 | align="center" | [http://www.portaudio.com/ portaudio]
 | align="center" | -
-| align="center" | 190600_20161030, 190700_20210406
+| align="center" | 190700_20210406, 190600_20161030
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PortAudio is a free, cross-platform, open-source, audio I/O library. It lets you write simple audio programs in 'C' or C++ that will compile and run on many platforms including Windows, Macintosh OS X, and Unix (OSS/ALSA). It is intended to promote the exchange of audio software between developers on different platforms. Many applications use PortAudio for Audio I/O. Homepage: http://www.portaudio.com/ URL: http://www.portaudio.com/ Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: PyAudio-0.2.13<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PortAudio is a free, cross-platform, open-source, audio I/O library. It lets you write simple audio programs in 'C' or C++ that will compile and run on many platforms including Windows, Macintosh OS X, and Unix (OSS/ALSA). It is intended to promote the exchange of audio software between developers on different platforms. Many applications use PortAudio for Audio I/O. Homepage: http://www.portaudio.com/ URL: http://www.portaudio.com/ Compatible modules: python/3.6, python/3.7, python/3.8 Extensions: PyAudio-0.2.11<br /><br /><br /></div>
 |-
 | align="center" | [https://www.postgresql.org/ postgresql]
 | align="center" | tools
-| align="center" | 9.6.6, 10.2, 10.3, 11.6, 12.1, 12.4, 13.2, 14.2, 16.0
+| align="center" | 12.4, 13.2, 14.2, 16.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation. Homepage: https://www.postgresql.org/ URL: https://www.postgresql.org/ Compatible modules: python/3.10, python/3.11 Extensions: psycopg2-2.9.9 Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://www.povray.org/ pov-ray]
 | align="center" | -
-| align="center" | 3.8.0-x.10064738, 3.7.0.7, 3.7.0.10
+| align="center" | 3.8.0-x.10064738, 3.7.0.10
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports. Homepage: https://www.povray.org/ URL: https://www.povray.org/<br /><br /><br /></div>
-|-
-| align="center" | [http://www.povray.org/ povray]
-| align="center" | vis
-| align="center" | 3.7.0.7
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports. Homepage: http://www.povray.org/ Keyword:vis<br /><br /><br /></div>
 |-
 | align="center" | [http://matsen.fhcrc.org/pplacer/ pplacer]
@@ Line 4,178: / Line 3,563: @@
 | align="center" | bio
 | align="center" | 0.20.4
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A bioinformatics tool to PRe-process and show INformation of SEQuence data. Homepage: http://prinseq.sourceforge.net Extensions: Cairo-1.106, Contextual::Return-0.004008, Digest::MD5-2.54, ExtUtils::Depends-0.405, ExtUtils::PkgConfig-1.15, File::Spec-3.62, File::Temp-0.2304, Getopt::Long-2.48, JSON-2.90, Math::Cephes::Matrix-0.5304, Math::MatrixReal-2.12, MIME::Base64-3.15, Pod::Usage-1.68, Statistics::PCA-0.0.1, Text::SimpleTable-2.03, Want-0.26 Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A bioinformatics tool to PRe-process and show INformation of SEQuence data. Homepage: http://prinseq.sourceforge.net URL: http://prinseq.sourceforge.net Extensions: Cairo-1.109, Contextual::Return-0.2.1, ExtUtils::Depends-0.8001, ExtUtils::PkgConfig-1.16, Math::Cephes::Matrix-0.5305, Math::MatrixReal-2.13, MIME::Base64-3.15, Pod::Usage-2.0, Statistics::PCA-0.0.1, Text::SimpleTable-2.07 Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://www.prismmodelchecker.org/ prism]
@@ Line 4,184: / Line 3,569: @@
 | align="center" | 4.7
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PRISM is a probabilistic model checker, a tool for formal modelling and analysis of systems that exhibit random or probabilistic behaviour. It has been used to analyse systems from many different application domains, including communication and multimedia protocols, randomised distributed algorithms, security protocols, biological systems and many others. Homepage: https://www.prismmodelchecker.org/ URL: https://www.prismmodelchecker.org/<br /><br /><br /></div>
-|-
-| align="center" | [https://sourceforge.net/projects/probmask/ probmask]
-| align="center" | -
-| align="center" | 2011.12
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Probmask (ZORRO) is a probabilistic alignment masking program Homepage: https://sourceforge.net/projects/probmask/<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/hyattpd/Prodigal/ prodigal]
@@ Line 4,202: / Line 3,582: @@
 | align="center" | [https://proj.org proj]
 | align="center" | geo
-| align="center" | 4.9.3, 5.1.0, 5.2.0, 6.0.0, 6.3.0, 6.3.2, 7.0.0, 7.0.1, 7.2.1, 8.0.0, 9.0.0, 9.0.1, 9.2.0, 9.4.1
+| align="center" | 4.9.3, 6.3.2, 7.0.0, 7.0.1, 7.2.1, 8.0.0, 9.0.0, 9.0.1, 9.2.0, 9.4.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates Homepage: https://proj.org URL: https://proj.org Compatible modules: python/3.10, python/3.11, python/3.12 Extensions: pyproj-3.6.1 Keyword:geo<br /><br /><br /></div>
 |-
@@ Line 4,208: / Line 3,588: @@
 | align="center" | geo
 | align="center" | 1.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: proj4-fortran is a f77 and f90 wrappers for proj4, a cartograohic projections library. Homepage: https://github.com/mhagdorn/proj4-fortran Keyword:geo<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: proj4-fortran is a f77 and f90 wrappers for proj4, a cartograohic projections library. Homepage: https://github.com/mhagdorn/proj4-fortran URL: https://github.com/mhagdorn/proj4-fortran Keyword:geo<br /><br /><br /></div>
 |-
 | align="center" | [https://www.vicbioinformatics.com/software.prokka.shtml prokka]
@@ Line 4,214: / Line 3,594: @@
 | align="center" | 1.14.5
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Prokka is a software tool for the rapid annotation of prokaryotic genomes. Homepage: https://www.vicbioinformatics.com/software.prokka.shtml URL: https://www.vicbioinformatics.com/software.prokka.shtml<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/BioInf-Wuerzburg/proovread proovread]
-| align="center" | bio
-| align="center" | 2.14.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PacBio hybrid error correction through iterative short read consensus Homepage: https://github.com/BioInf-Wuerzburg/proovread Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/google/protobuf/ protobuf]
 | align="center" | tools
-| align="center" | 3.3.0, 3.6.1, 3.7.1, 3.9.1, 3.11.1, 3.12.3, 3.19.4, 3.21.3, 24.4
+| align="center" | 3.12.3, 3.19.4, 3.21.3, 24.4
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Google Protocol Buffers Homepage: https://github.com/google/protobuf/ URL: https://github.com/google/protobuf/ Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 4,237: / Line 3,612: @@
 | align="center" | [http://www.psicode.org/ psi4]
 | align="center" | chem
-| align="center" | 1.1, 1.3.2, 1.4, 1.5, 1.9
+| align="center" | 1.3.2, 1.4, 1.5, 1.9
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel. Homepage: http://www.psicode.org/ URL: http://www.psicode.org/ Compatible modules: python/3.10, python/3.11 Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 4,248: / Line 3,623: @@
 | align="center" | bio
 | align="center" | 0.6.5
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This software package infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model. Homepage: https://github.com/lh3/psmc Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This software package infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model. Homepage: https://github.com/lh3/psmc URL: https://github.com/lh3/psmc Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://ptex.us/ ptex]
@@ Line 4,277: / Line 3,652: @@
 | align="center" | [https://python.org/ python]
 | align="center" | tools
-| align="center" | 2.7.13, 2.7.14, 2.7.18, 3.5.2, 3.5.4, 3.6.3, 3.6.10, 3.7.0, 3.7.4, 3.7.7, 3.7.9, 3.8.0, 3.8.2, 3.8.10, 3.9.6, 3.10.2, 3.10.13, 3.11.2, 3.11.5, 3.12.4
+| align="center" | 2.7.18, 3.6.10, 3.7.7, 3.7.9, 3.8.2, 3.8.10, 3.9.6, 3.10.2, 3.10.13, 3.11.2, 3.11.5, 3.12.4
 | Documentation: [[Python]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. Homepage: https://python.org/ URL: https://python.org/ Extensions: distlib-0.3.8, filelock-3.13.4, flit_core-3.9.0, hatch_vcs-0.4.0, hatchling-1.24.2, packaging-24.0, pathspec-0.12.1, pip-24.0, platformdirs-4.2.0, pluggy-1.5.0, setuptools-70.0.0, setuptools-scm-8.0.4, tomli-2.0.1, trove-classifiers-2024.4.10, typing_extensions-4.12.1, virtualenv-20.26.2, wheel-0.43.0 Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 4,292: / Line 3,667: @@
 | align="center" | [https://userbase.kde.org/QCA qca]
 | align="center" | geo
-| align="center" | 2.1.3, 2.3.0, 2.3.5, 2.3.7
+| align="center" | 2.3.0, 2.3.5, 2.3.7
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Taking a hint from the similarly-named Java Cryptography Architecture, QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers. The advantage of this model is to allow applications to avoid linking to or explicitly depending on any particular cryptographic library. This allows one to easily change or upgrade crypto implementations without even needing to recompile the application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX. Homepage: https://userbase.kde.org/QCA URL: https://userbase.kde.org/QCA Keyword:geo<br /><br /><br /></div>
 |-
@@ Line 4,307: / Line 3,682: @@
 | align="center" | [http://www.qgis.org/ qgis]
 | align="center" | geo
-| align="center" | 2.18.24, 3.10.6, 3.22.14, 3.28.12
+| align="center" | 3.10.6, 3.22.14, 3.28.12
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: QGIS is a user friendly Open Source Geographic Information System (GIS) Homepage: http://www.qgis.org/ URL: http://www.qgis.org/ Compatible modules: python/3.11, python/3.10 Extensions: OWSLib-0.29.3, psycopg2-2.9.9, PyYAML-6.0.1 Keyword:geo<br /><br /><br /></div>
 |-
 | align="center" | [http://www.qhull.org qhull]
 | align="center" | math
-| align="center" | 2015.2, 2019.1, 2020.2
+| align="center" | 2019.1, 2020.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. Homepage: http://www.qhull.org URL: http://www.qhull.org Keyword:math<br /><br /><br /></div>
 |-
@@ Line 4,328: / Line 3,703: @@
 | align="center" | math
 | align="center" | 1.1.2
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. Homepage: https://sourceforge.net/projects/qrupdate/ Keyword:math<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. Homepage: https://sourceforge.net/projects/qrupdate/ URL: https://sourceforge.net/projects/qrupdate/ Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [https://www.riverbankcomputing.com/software/qscintilla qscintilla]
 | align="center" | tools
-| align="center" | 2.10.7, 2.11.2, 2.11.6, 2.14.1
+| align="center" | 2.11.2, 2.11.6, 2.14.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control Homepage: https://www.riverbankcomputing.com/software/qscintilla URL: https://www.riverbankcomputing.com/software/qscintilla Compatible modules: python/3.10, python/3.11 Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://qt.io/ qt]
 | align="center" | tools
-| align="center" | 3.3.8, 4.8.7, 5.6.1, 5.9.6, 5.10.1, 5.11.3, 5.12.3, 5.12.8, 5.13.1, 5.15.2, 5.15.8, 5.15.11
+| align="center" | 5.12.8, 5.15.2, 5.15.8, 5.15.11
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Qt is a comprehensive cross-platform C++ application framework. Homepage: https://qt.io/ URL: https://qt.io/ Compatible modules: python/3.10, python/3.11 Extensions: ply-3.11, PyQt-builder-1.15.3, PyQt5-5.15.10, PyQt5_sip-12.13.0, PyQtWebEngine-5.15.6, SIP-6.7.12, toml-0.10.2 Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 4,362: / Line 3,737: @@
 | align="center" | [https://www.quantum-espresso.org quantumespresso]
 | align="center" | chem
-| align="center" | 6.2.2, 6.3, 6.4.1, 6.5, 6.6, 6.7, 6.8, 7.0, 7.1, 7.2, 7.3.1
+| align="center" | 6.5, 6.6, 6.7, 6.8, 7.0, 7.1, 7.2, 7.3.1
 | Documentation: [[Quantum ESPRESSO]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). Homepage: https://www.quantum-espresso.org URL: https://www.quantum-espresso.org Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 4,370: / Line 3,745: @@
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitable for comparison. Homepage: https://github.com/ablab/quast URL: https://github.com/ablab/quast Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: joblib-0.17.0, QUAST-5.2.0, semantic-version-2.8.5, simplejson-3.17.0, toml-0.10.2<br /><br /><br /></div>
 |-
-| align="center" | [http://www.genome.umd.edu/quorum.html quorum]
+| align="center" | [https://qwt.sourceforge.io/ qwt]
-| align="center" | bio
-| align="center" | 1.1.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: QuorUM is an error corrector for Illumina reads Homepage: http://www.genome.umd.edu/quorum.html Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://qwt.sourceforge.net/ qwt]
 | align="center" | tools
-| align="center" | 6.1.3, 6.1.4, 6.2.0
+| align="center" | 6.1.4, 6.2.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Homepage: http://qwt.sourceforge.net/ URL: http://qwt.sourceforge.net/ Keyword:tools<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Homepage: https://qwt.sourceforge.io/ URL: https://qwt.sourceforge.io/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [http://qwtpolar.sourceforge.net/ qwtpolar]
@@ Line 4,387: / Line 3,757: @@
 | align="center" | [https://www.r-project.org/ r]
 | align="center" | tools
-| align="center" | 3.4.4, 3.5.1, 3.5.2, 3.6.0, 3.6.1, 4.0.0, 4.0.2, 4.0.5, 4.1.0, 4.1.2, 4.2.1, 4.2.2, 4.3.1, 4.4.0
+| align="center" | 4.0.0, 4.0.2, 4.0.5, 4.1.0, 4.1.2, 4.2.1, 4.2.2, 4.3.1, 4.4.0
 | Documentation: [[R]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: R is a free software environment for statistical computing and graphics. Homepage: https://www.r-project.org/ URL: https://www.r-project.org/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://bioconductor.org r-bundle-bioconductor]
 | align="center" | bio
-| align="center" | 3.8, 3.9, 3.12, 3.14, 3.16, 3.17, 3.18
+| align="center" | 3.12, 3.14, 3.16, 3.17, 3.18
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data. Homepage: https://bioconductor.org URL: https://bioconductor.org Extensions: abind-1.4-5, ade4-1.7-22, admisc-0.34, affxparser-1.74.0, affy-1.80.0, affycoretools-1.74.0, affyio-1.72.0, AgiMicroRna-2.52.0, agricolae-1.3-7, ALDEx2-1.34.0, AlgDesign-1.2.1, ALL-1.44.0, annaffy-1.74.0, annotate-1.80.0, AnnotationDbi-1.64.1, AnnotationFilter-1.26.0, AnnotationForge-1.44.0, AnnotationHub-3.10.0, anytime-0.3.9, aod-1.3.3, ape-5.7-1, aroma.affymetrix-3.2.1, aroma.apd-0.7.0, aroma.core-3.3.0, aroma.light-3.32.0, ash-1.0-15, askpass-1.2.0, assertthat-0.2.1, ATACseqQC-1.26.0, aws-2.5-3, aws.s3-0.3.21, aws.signature-0.6.0, awsMethods-1.1-1, backports-1.4.1, ballgown-2.34.0, base64-2.0.1, base64enc-0.1-3, basilisk-1.14.1, basilisk.utils-1.14.1, batchelor-1.18.1, baySeq-2.36.0, BBmisc-1.13, beachmat-2.18.0, beanplot-1.3.1, beeswarm-0.4.0, BH-1.81.0-1, BiasedUrn-2.0.11, Biobase-2.62.0, BiocBaseUtils-1.4.0, BiocFileCache-2.10.1, BiocGenerics-0.48.1, BiocIO-1.12.0, BiocManager-1.30.22, BiocNeighbors-1.20.2, BiocParallel-1.36.0, BiocSingular-1.18.0, BiocStyle-2.30.0, BiocVersion-3.18.1, biomaRt-2.58.0, biomformat-1.30.0, Biostrings-2.70.1, biovizBase-1.50.0, bit-4.0.5, bit64-4.0.5, bitops-1.0-7, blme-1.0-5, blob-1.2.4, bluster-1.12.0, bookdown-0.37, boot-1.3-28.1, brio-1.1.4, broom-1.0.5, broom.helpers-1.14.0, BSgenome-1.70.1, BSgenome.Cfamiliaris.UCSC.canFam3-1.4.0, BSgenome.Hsapiens.UCSC.hg19-1.4.3, BSgenome.Hsapiens.UCSC.hg38-1.4.5, BSgenome.Mmusculus.UCSC.mm10-1.4.3, bslib-0.6.1, bumphunter-1.44.0, ca-0.71.1, cachem-1.0.8, Cairo-1.6-2, calibrate-1.7.7, callr-3.7.3, CAMERA-1.58.0, car-3.1-2, carData-3.0-5, caret-6.0-94, Category-2.68.0, caTools-1.18.2, ccdata-1.28.0, ccmap-1.28.0, cellranger-1.1.0, CGHbase-1.62.0, checkmate-2.3.1, ChIPpeakAnno-3.36.0, circlize-0.4.15, class-7.3-22, classInt-0.4-10, cli-3.6.2, clipr-0.8.0, clock-0.7.0, clue-0.3-65, cluster-2.1.6, CNEr-1.38.0, coda-0.19-4, codetools-0.2-19, coloc-5.2.3, colorRamps-2.3.1, colorspace-2.1-0, colourpicker-1.3.0, combinat-0.0-8, commonmark-1.9.0, ComplexHeatmap-2.18.0, ConsensusClusterPlus-1.66.0, conumee-1.36.0, corpcor-1.6.10, corrplot-0.92, cowplot-1.1.2, cpp11-0.4.7, crayon-1.5.2, crossmeta-1.28.0, crosstalk-1.2.1, cummeRbund-2.44.0, curl-5.2.0, cytolib-2.14.0, CytoML-2.14.0, dada2-1.30.0, data.table-1.14.10, DBI-1.2.0, dbplyr-2.4.0, DeconRNASeq-1.44.0, DEGseq-1.56.1, DelayedArray-0.28.0, DelayedMatrixStats-1.24.0, deldir-2.0-2, dendextend-1.17.1, densvis-1.12.0, DEoptimR-1.1-3, derfinder-1.36.0, derfinderHelper-1.36.0, desc-1.4.3, DESeq2-1.42.0, deSolve-1.40, diagram-1.6.5, dichromat-2.0-0.1, diffcyt-1.22.0, diffobj-0.3.5, digest-0.6.33, diptest-0.77-0, dir.expiry-1.10.0, directlabels-2023.8.25, DirichletMultinomial-1.44.0, DNAcopy-1.76.0, docopt-0.7.1, doParallel-1.0.17, doRNG-1.8.6, dotCall64-1.1-1, dplyr-1.1.4, dqrng-0.3.2, DRIMSeq-1.30.0, DropletUtils-1.22.0, DT-0.31, dupRadar-1.32.0, DynDoc-1.80.0, e1071-1.7-14, EBImage-4.44.0, edgeR-4.0.6, egg-0.4.5, ellipse-0.5.0, ellipsis-0.3.2, emmeans-1.9.0, EnsDb.Hsapiens.v75-2.99.0, EnsDb.Hsapiens.v86-2.99.0, ensembldb-2.26.0, EnvStats-2.8.1, estimability-1.4.1, evaluate-0.23, ExperimentHub-2.10.0, extraDistr-1.10.0, fANCOVA-0.6-1, fansi-1.0.6, farver-2.1.1, fastcluster-1.2.3, fastDummies-1.7.3, fastICA-1.2-4, fastmap-1.1.1, fastmatch-1.1-4, fda-6.1.4, FDb.InfiniumMethylation.hg19-2.2.0, fdrtool-1.2.17, fds-1.8, ff-4.0.9, fftwtools-0.9-11, fgsea-1.28.0, filelock-1.0.3, fitdistrplus-1.1-11, flexmix-2.3-19, flowClust-3.40.0, flowCore-2.14.0, FlowSOM-2.10.0, FlowSorted.Blood.EPIC-2.6.0, FlowSorted.CordBloodCombined.450k-1.18.0, flowStats-4.14.0, flowViz-1.66.0, flowWorkspace-4.14.1, FNN-1.1.3.2, fontawesome-0.5.2, forcats-1.0.0, foreach-1.5.2, foreign-0.8-86, formatR-1.14, Formula-1.2-5, formula.tools-1.7.1, fpc-2.2-11, FRASER-1.14.0, fresh-0.2.0, fs-1.6.3, futile.logger-1.4.3, futile.options-1.0.1, future-1.33.1, future.apply-1.11.1, gbm-2.1.8.1, gclus-1.3.2, gcrma-2.74.0, gdata-3.0.0, gdsfmt-1.38.0, genefilter-1.84.0, geneLenDataBase-1.38.0, geneplotter-1.80.0, generics-0.1.3, GENESIS-2.32.0, GENIE3-1.24.0, GenomeInfoDb-1.38.5, GenomeInfoDbData-1.2.11, GenomicAlignments-1.38.1, GenomicFeatures-1.54.1, GenomicFiles-1.38.0, GenomicRanges-1.54.1, GenomicScores-2.14.3, GEOquery-2.70.0, GetoptLong-1.0.5, GGally-2.2.0, ggbeeswarm-0.7.2, ggbio-1.50.0, ggcyto-1.30.0, ggdendro-0.1.23, ggforce-0.4.1, ggnewscale-0.4.9, ggplot2-3.4.4, ggpointdensity-0.1.0, ggpubr-0.6.0, ggrastr-1.0.2, ggrepel-0.9.4, ggridges-0.5.5, ggsci-3.0.0, ggseqlogo-0.1, ggsignif-0.6.4, ggstats-0.5.1, ggthemes-5.0.0, ggvis-0.4.8, GLAD-2.66.0, Glimma-2.12.0, glmmTMB-1.1.8, glmnet-4.1-8, GlobalAncova-4.20.0, GlobalOptions-0.1.2, globals-0.16.2, globaltest-5.56.0, glue-1.7.0, GO.db-3.18.0, goftest-1.2-3, goseq-1.54.0, GOstats-2.68.0, gower-1.0.1, gplots-3.1.3, graph-1.80.0, gridExtra-2.3, GSA-1.03.2, GSEABase-1.64.0, gsl-2.1-8, gsmoothr-0.1.7, GSVA-1.50.0, gtable-0.3.4, gtools-3.9.5, Gviz-1.46.1, GWASExactHW-1.01, GWASTools-1.48.0, hardhat-1.3.0, haven-2.5.4, HDF5Array-1.30.0, hdrcde-3.4, heatmaply-1.5.0, here-1.0.1, hexbin-1.28.3, hgu133plus2.db-3.13.0, highr-0.10, Hmisc-5.1-1, HMMcopy-1.44.0, hms-1.1.3, Homo.sapiens-1.3.1, htmlTable-2.4.2, htmltools-0.5.7, htmlwidgets-1.6.4, httpuv-1.6.13, httr-1.4.7, hwriter-1.3.2.1, ica-1.0-3, IDPmisc-1.1.20, igraph-1.6.0, IHW-1.30.0, IlluminaHumanMethylation450kanno.ilmn12.hg19-0.6.1, IlluminaHumanMethylation450kmanifest-0.4.0, IlluminaHumanMethylationEPICanno.ilm10b2.hg19-0.6.0, IlluminaHumanMethylationEPICanno.ilm10b4.hg19-0.6.0, IlluminaHumanMethylationEPICmanifest-0.3.0, illuminaio-0.44.0, impute-1.76.0, InteractionSet-1.30.0, interactiveDisplayBase-1.40.0, interp-1.1-5, ipred-0.9-14, IRanges-2.36.0, irlba-2.3.5.1, isoband-0.2.7, isva-1.9, iterators-1.0.14, itertools-0.1-3, JADE-2.0-4, jomo-2.7-6, jpeg-0.1-10, jquerylib-0.1.4, jsonlite-1.8.8, KEGG.db-3.2.4, KEGGgraph-1.62.0, KEGGREST-1.42.0, kernlab-0.9-32, KernSmooth-2.23-22, klaR-1.7-3, knitr-1.45, ks-1.14.1, labeling-0.4.3, labelled-2.12.0, lambda.r-1.2.4, LaplacesDemon-16.1.6, later-1.3.2, lattice-0.22-5, latticeExtra-0.6-30, lava-1.7.3, lazyeval-0.2.2, LEA-3.14.0, leiden-0.4.3.1, lifecycle-1.0.4, limma-3.58.1, limSolve-1.5.7, listenv-0.9.0, lme4-1.1-35.1, lmerTest-3.1-3, lmtest-0.9-40, locfit-1.5-9.8, logistf-1.26.0, logspline-2.1.21, lpSolve-5.6.20, lpsymphony-1.30.0, lsa-0.73.3, lubridate-1.9.3, lumi-2.54.0, magrittr-2.0.3, MALDIquant-1.22.1, markdown-1.12, marray-1.80.0, maSigPro-1.74.0, MASS-7.3-60, MassSpecWavelet-1.68.0, mathjaxr-1.6-0, Matrix-1.6-4, MatrixGenerics-1.14.0, MatrixModels-0.5-3, matrixStats-1.2.0, mclust-6.0.1, MEDIPS-1.54.0, memoise-2.0.1, MetaboCoreUtils-1.10.0, metagenomeSeq-1.43.0, metaMA-3.1.3, metap-1.9, metapod-1.10.1, MethylSeekR-1.42.0, methylumi-2.48.0, Mfuzz-2.62.0, mgcv-1.9-1, mhsmm-0.4.21, mice-3.16.0, mime-0.12, minfi-1.48.0, miniUI-0.1.1.1, minqa-1.2.6, misc3d-0.9-1, missForest-1.5, missMethyl-1.36.0, mitml-0.4-5, mixOmics-6.26.0, mixsqp-0.3-54, mixtools-2.0.0, mlbench-2.1-3.1, MLInterfaces-1.82.0, mnormt-2.1.1, ModelMetrics-1.2.2.2, modeltools-0.2-23, MotifDb-1.44.0, motifmatchr-1.24.0, motifStack-1.46.0, MsCoreUtils-1.14.1, MsExperiment-1.4.0, MsFeatures-1.10.0, MSnbase-2.28.1, multcomp-1.4-25, MultiAssayExperiment-1.28.0, multicool-1.0.0, MultiDataSet-1.30.0, multtest-2.58.0, munsell-0.5.0, muscat-1.16.0, mutoss-0.1-13, mvtnorm-1.2-4, mzID-1.40.0, mzR-2.36.0, NADA-1.6-1.1, ncdf4-1.22, ncdfFlow-2.48.0, NCmisc-1.2.0, nleqslv-3.3.5, nlme-3.1-164, nloptr-2.0.3, nnet-7.3-19, NOISeq-2.46.0, nor1mix-1.3-2, nortest-1.0-4, numDeriv-2016.8-1.1, oligo-1.66.0, oligoClasses-1.64.0, ontologyIndex-2.11, openCyto-2.14.0, openssl-2.1.1, openxlsx-4.2.5.2, operator.tools-1.6.3, ordinal-2023.12-4, org.Hs.eg.db-3.18.0, org.Mm.eg.db-3.18.0, org.Rn.eg.db-3.18.0, OrganismDbi-1.44.0, OUTRIDER-1.20.0, pan-1.9, parallelly-1.36.0, patchwork-1.2.0, pbapply-1.7-2, pbkrtest-0.5.2, pcaMethods-1.94.0, pcaPP-2.0-4, perm-1.0-0.4, permute-0.9-7, PFAM.db-3.18.0, pheatmap-1.0.12, phyloseq-1.46.0, pillar-1.9.0, pixmap-0.4-12, pkgbuild-1.4.3, pkgconfig-2.0.3, pkgload-1.3.3, plogr-0.2.0, plot3D-1.4, plotly-4.10.3, plotrix-3.8-4, pls-2.8-3, plyr-1.8.9, pmp-1.14.0, png-0.1-8, polyclip-1.10-6, polyester-1.38.0, polynom-1.4-1, poweRlaw-0.70.6, prabclus-2.3-3, pracma-2.4.4, praise-1.0.0, preprocessCore-1.64.0, preseqR-4.0.0, prettyunits-1.2.0, pROC-1.18.5, processx-3.8.3, prodlim-2023.08.28, progress-1.2.3, progressr-0.14.0, pRoloc-1.42.0, pRolocdata-1.40.0, pRolocGUI-2.12.0, promises-1.2.1, ProtGenerics-1.34.0, proxy-0.4-27, PRROC-1.3.1, ps-1.7.5, PSCBS-0.66.0, PureCN-2.8.1, purrr-1.0.2, qap-0.1-2, QFeatures-1.12.0, qlcMatrix-0.9.7, qqconf-1.3.2, qqman-0.1.9, quadprog-1.5-8, quantreg-5.97, quantsmooth-1.68.0, questionr-0.7.8, qvalue-2.34.0, R.cache-0.16.0, R.devices-2.17.1, R.filesets-2.15.0, R.huge-0.10.0, R.methodsS3-1.8.2, R.oo-1.25.0, R.rsp-0.45.0, R.utils-2.12.3, R6-2.5.1, ragg-1.2.7, rainbow-3.7, randomcoloR-1.1.0.1, randomForest-4.7-1.1, RANN-2.6.1, rappdirs-0.3.3, rARPACK-0.11-0, RBGL-1.78.0, rbibutils-2.2.16, RColorBrewer-1.1-3, Rcpp-1.0.12, RcppAnnoy-0.0.21, RcppArmadillo-0.12.6.6.1, RcppEigen-0.3.3.9.4, RcppGSL-0.3.13, RcppHNSW-0.5.0, RcppML-0.3.7, RcppParallel-5.1.7, RcppProgress-0.4.2, RcppRoll-0.3.0, RcppTOML-0.2.2, RcppZiggurat-0.1.6, RCurl-1.98-1.14, Rdpack-2.6, reader-1.0.6, readr-2.1.4, readxl-1.4.3, recipes-1.0.9, regioneR-1.34.0, registry-0.5-1, remaCor-0.0.16, rematch-2.0.0, rematch2-2.1.2, Repitools-1.48.0, ReportingTools-2.42.3, reshape-0.8.9, reshape2-1.4.4, ResidualMatrix-1.12.0, restfulr-0.0.15, reticulate-1.34.0, Rfast-2.1.0, rGADEM-2.50.0, Rgraphviz-2.46.0, rhdf5-2.46.1, rhdf5filters-1.14.1, Rhdf5lib-1.24.1, RhpcBLASctl-0.23-42, Rhtslib-2.4.0, Ringo-1.66.0, rjson-0.2.21, rlang-1.1.3, rmarkdown-2.25, RNASeqPower-1.42.0, rngtools-1.5.2, robustbase-0.99-1, ROC-1.78.0, ROCR-1.0-11, rols-2.30.0, ropls-1.34.0, rpart-4.1.23, rprojroot-2.0.4, RProtoBufLib-2.14.0, rrcov-1.7-4, Rsamtools-2.18.0, Rsolnp-1.16, RSpectra-0.16-1, RSQLite-2.3.4, rstatix-0.7.2, rstudioapi-0.15.0, Rsubread-2.16.0, rsvd-1.0.5, rtracklayer-1.62.0, Rtsne-0.17, ruv-0.9.7.1, S4Arrays-1.2.0, S4Vectors-0.40.2, sampling-2.10, samr-3.0, sandwich-3.1-0, sass-0.4.8, SC3-1.30.0, ScaledMatrix-1.10.0, scales-1.3.0, SCANVIS-1.16.0, scater-1.30.1, scattermore-1.2, scran-1.30.0, scrime-1.3.5, sctransform-0.4.1, scuttle-1.12.0, segmented-2.0-1, SeqArray-1.42.0, seqLogo-1.68.0, SeqVarTools-1.40.0, seriation-1.5.4, Seurat-5.0.1, SeuratObject-5.0.1, sfsmisc-1.1-16, shape-1.4.6, shiny-1.8.0, shinyBS-0.61.1, shinydashboard-0.7.2, shinydashboardPlus-2.0.3, shinyFiles-0.9.3, shinyhelper-0.3.2, shinyjs-2.1.0, shinypanel-0.1.5, shinyWidgets-0.8.1, ShortRead-1.60.0, siggenes-1.76.0, Signac-1.12.0, SingleCellExperiment-1.24.0, SingleR-2.4.1, sitmo-2.0.2, slam-0.1-50, SMVar-1.3.4, sn-2.1.1, snow-0.4-4, SnowballC-0.7.1, SNPRelate-1.36.0, snpStats-1.52.0, sourcetools-0.1.7-1, sp-2.1-2, spam-2.10-0, SparseArray-1.2.3, SparseM-1.81, sparseMatrixStats-1.14.0, sparsesvd-0.2-2, spatstat.data-3.0-3, spatstat.explore-3.2-5, spatstat.geom-3.2-7, spatstat.random-3.2-2, spatstat.sparse-3.0-3, spatstat.utils-3.0-4, Spectra-1.12.0, SPIA-2.54.0, splitstackshape-1.4.8, SQUAREM-2021.1, stageR-1.24.0, statmod-1.5.0, stringi-1.8.3, stringr-1.5.1, struct-1.14.0, structToolbox-1.14.0, styler-1.10.2, SummarizedExperiment-1.32.0, survival-3.5-7, susieR-0.12.35, sva-3.50.0, sys-3.4.2, systemfonts-1.0.5, tensor-1.5, testthat-3.2.1, textshaping-0.3.7, TFBSTools-1.40.0, TFisher-0.2.0, TFMPvalue-0.0.9, TH.data-1.1-2, threejs-0.3.3, tibble-3.2.1, tidyr-1.3.0, tidyselect-1.2.0, tiff-0.1-12, timechange-0.2.0, timeDate-4032.109, tinytex-0.49, tkWidgets-1.80.0, TMB-1.9.10, truncnorm-1.0-9, TSP-1.2-4, tweenr-2.0.2, TxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2, TxDb.Mmusculus.UCSC.mm10.knownGene-3.10.0, tximport-1.30.0, tzdb-0.4.0, ucminf-1.2.1, utf8-1.2.4, uwot-0.1.16, V8-4.4.1, variancePartition-1.32.2, VariantAnnotation-1.48.1, vctrs-0.6.5, vegan-2.6-4, venn-1.12, VennDiagram-1.7.3, VGAM-1.1-9, vipor-0.4.7, viridis-0.6.4, viridisLite-0.4.2, vroom-1.6.5, vsn-3.70.0, waiter-0.2.5, waldo-0.5.2, wateRmelon-2.8.0, webshot-0.5.5, widgetTools-1.80.0, withr-2.5.2, Wrench-1.20.0, WriteXLS-6.5.0, xcms-4.0.1, xfun-0.41, xgboost-1.7.6.1, XML-3.99-0.16, xml2-1.3.6, xtable-1.8-4, XVector-0.42.0, yaml-2.3.8, zCompositions-1.5.0-1, zip-2.3.0, zlibbioc-1.48.0, zoo-1.8-12 Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 4,409: / Line 3,779: @@
 | align="center" | 1.4.3, 1.4.13, 1.5.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. Homepage: https://github.com/lbcb-sci/racon URL: https://github.com/lbcb-sci/racon Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://bioinformatics.psb.ugent.be/software/details/Randfold randfold]
-| align="center" | bio
-| align="center" | 2.0.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Minimum free energy of folding randomization test software Homepage: http://bioinformatics.psb.ugent.be/software/details/Randfold Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://randomlib.sourceforge.net/html/ randomlib]
@@ Line 4,434: / Line 3,799: @@
 | align="center" | 0.9.0, 0.10.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Raqm is a small library that encapsulates the logic for complex text layout and provides a convenient API. Homepage: https://github.com/HOST-Oman/libraqm URL: https://github.com/HOST-Oman/libraqm<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/statgen/Raremetal raremetal]
-| align="center" | -
-| align="center" | 4.15.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A tool for rare variants meta-analysis Homepage: https://github.com/statgen/Raremetal URL: https://github.com/statgen/Raremetal<br /><br /><br /></div>
 |-
 | align="center" | [https://iraspa.org/raspa/ raspa2]
@@ Line 4,457: / Line 3,817: @@
 | align="center" | [https://github.com/stamatak/standard-RAxML raxml]
 | align="center" | bio
-| align="center" | 8.2.11, 8.2.12
+| align="center" | 8.2.12
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. Homepage: https://github.com/stamatak/standard-RAxML URL: https://github.com/stamatak/standard-RAxML Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/amkozlov/raxml-ng raxml-ng]
 | align="center" | -
-| align="center" | 0.9.0, 1.0.1, 1.2.0
+| align="center" | 1.0.1, 1.2.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. Homepage: https://github.com/amkozlov/raxml-ng URL: https://github.com/amkozlov/raxml-ng<br /><br /><br /></div>
 |-
@@ Line 4,472: / Line 3,832: @@
 | align="center" | [https://github.com/zorino/ray ray]
 | align="center" | bio
-| align="center" | 3.0.0, 3.0.1
+| align="center" | 3.0.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Ray -- Parallel genome assemblies for parallel DNA sequencing. Homepage: https://github.com/zorino/ray URL: https://github.com/zorino/ray Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 4,482: / Line 3,842: @@
 | align="center" | [http://www.rdkit.org/ rdkit]
 | align="center" | chem
-| align="center" | 2018.03.3, 2019.03.4, 2020.09.1b1, 2021.03.3, 2021.09.3, 2021.09.4, 2022.09.4, 2023.09.3
+| align="center" | 2019.03.4, 2020.09.1b1, 2021.03.3, 2021.09.3, 2021.09.4, 2022.09.4, 2023.09.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python. Homepage: http://www.rdkit.org/ URL: http://www.rdkit.org/ Compatible modules: python/3.10, python/3.11 Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://re2c.org/ re2c]
 | align="center" | -
-| align="center" | 1.2.1, 1.3
+| align="center" | 1.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: re2c is a free and open-source lexer generator for C and C++. Its main goal is generating fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using traditional table-driven approach, re2c encodes the generated finite state automata directly in the form of conditional jumps and comparisons. Homepage: https://re2c.org/ URL: https://re2c.org/<br /><br /><br /></div>
 |-
@@ Line 4,493: / Line 3,853: @@
 | align="center" | bio
 | align="center" | 1.08
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Proper identification of repetitive sequences is an essential step in genome analysis. The RECON package performs de novo identification and classification of repeat sequence families from genomic sequences. The underlying algorithm is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. Specifically, our extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. RECON should be useful for first-pass automatic classification of repeats in newly sequenced genomes. Homepage: http://eddylab.org/software/recon/ Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Proper identification of repetitive sequences is an essential step in genome analysis. The RECON package performs de novo identification and classification of repeat sequence families from genomic sequences. The underlying algorithm is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. Specifically, our extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. RECON should be useful for first-pass automatic classification of repeats in newly sequenced genomes. Homepage: http://eddylab.org/software/recon/ URL: http://eddylab.org/software/recon/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/rlabduke/reduce reduce]
 | align="center" | -
-| align="center" | 4.14, 20180820
+| align="center" | 4.14
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Reduce - tool for adding and correcting hydrogens in PDB files Homepage: https://github.com/rlabduke/reduce<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Reduce - tool for adding and correcting hydrogens in PDB files Homepage: https://github.com/rlabduke/reduce URL: https://github.com/rlabduke/reduce<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/eth-cscs/reframe reframe]
 | align="center" | -
-| align="center" | 2.21, 3.12.0
+| align="center" | 3.12.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ReFrame is a framework for writing regression tests for HPC systems. Homepage: https://github.com/eth-cscs/reframe URL: https://github.com/eth-cscs/reframe Compatible modules: python/3.8.10, python/3.9.6, python/3.10.2 Extensions: attrs-21.4.0, certifi-2021.10.8, chardet-4.0.0, idna-3.3, importlib_resources-5.7.1, jsonschema-4.4.0, pyrsistent-0.18.1, reframe-3.12.0, requests-2.27.1, semver-2.13.0, urllib3-1.26.9, zipp-3.8.0<br /><br /><br /></div>
 |-
@@ Line 4,512: / Line 3,872: @@
 | align="center" | [https://www3.mrc-lmb.cam.ac.uk/relion/ relion]
 | align="center" | chem
-| align="center" | 2.1.0, 3.0, 3.1.1, 4.0.0
+| align="center" | 3.1.1, 4.0.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. It is developed in the research group of Sjors Scheres at the MRC Laboratory of Molecular Biology. Homepage: https://www3.mrc-lmb.cam.ac.uk/relion/ URL: https://www3.mrc-lmb.cam.ac.uk/relion/ Keyword:chem<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/TACC/remora remora]
-| align="center" | tools
-| align="center" | 1.8.2, 1.8.3
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: REsource MOnitoring for Remote Applications Homepage: https://github.com/TACC/remora Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://repast.github.io/ repasthpc]
@@ Line 4,527: / Line 3,882: @@
 | align="center" | [http://www.repeatmasker.org/ repeatmasker]
 | align="center" | bio
-| align="center" | 4-0-9-p2, 4.1.2-p1, 4.1.0, 4.1.1
+| align="center" | 4.1.2-p1, 4.1.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. Homepage: http://www.repeatmasker.org/ URL: http://www.repeatmasker.org/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 4,554: / Line 3,909: @@
 | align="center" | 1.4.2, 1.10.0, 1.11.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel RenderKit common library Homepage: https://github.com/ospray/rkcommon URL: https://github.com/ospray/rkcommon<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/chedinlab/rlooper.git rlooper]
-| align="center" | -
-| align="center" | 1.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Extract sequences from a fastx file given a subsequence or identifier Homepage: https://github.com/chedinlab/rlooper.git<br /><br /><br /></div>
 |-
 | align="center" | [http://rnaseq-mats.sourceforge.net/ rmats]
 | align="center" | -
-| align="center" | 4.0.2, 4.1.1, 4.1.2
+| align="center" | 4.1.1, 4.1.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both paired and unpaired study design. Homepage: http://rnaseq-mats.sourceforge.net/ URL: http://rnaseq-mats.sourceforge.net/<br /><br /><br /></div>
 |-
 | align="center" | [http://www.repeatmasker.org/RMBlast.html rmblast]
 | align="center" | bio
-| align="center" | 2.9.0, 2.10.0
+| align="center" | 2.10.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' for use with RepeatMasker and RepeatModeler. Homepage: http://www.repeatmasker.org/RMBlast.html URL: http://www.repeatmasker.org/RMBlast.html Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 4,592: / Line 3,942: @@
 | align="center" | [https://root.cern.ch/drupal/ root]
 | align="center" | tools
-| align="center" | 5.34.36, 6.08.02, 6.14.04, 6.20.04, 6.24.06, 6.26.06, 6.28.06
+| align="center" | 6.20.04, 6.24.06, 6.26.06, 6.28.06
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. Homepage: https://root.cern.ch/drupal/ URL: https://root.cern.ch/drupal/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://www.rosettacommons.org rosetta]
 | align="center" | chem
-| align="center" | 3.9, 3.10, 3.12, 3.13, 2019.21.60746
+| align="center" | 3.10, 3.12, 3.13, 2019.21.60746
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids. This is a weekly release. Homepage: https://www.rosettacommons.org Keyword:chem<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids. This is a weekly release. Homepage: https://www.rosettacommons.org URL: https://www.rosettacommons.org Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [http://deweylab.github.io/RSEM/ rsem]
 | align="center" | bio
-| align="center" | 1.3.0, 1.3.3
+| align="center" | 1.3.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RNA-Seq by Expectation-Maximization Homepage: http://deweylab.github.io/RSEM/ URL: http://deweylab.github.io/RSEM/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://www.rstudio.com/ rstudio-server]
 | align="center" | tools
-| align="center" | 1.2.1335, 4.1, 4.2, 4.3, 2021.09.1+372
+| align="center" | 4.1, 4.2, 4.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RStudio Server enables you to provide a browser based interface to a version of R running on a remote Linux server, bringing the power and productivity of the RStudio IDE to server-based deployments of R. Homepage: https://www.rstudio.com/ URL: https://www.rstudio.com/ Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 4,622: / Line 3,972: @@
 | align="center" | [https://www.ruby-lang.org ruby]
 | align="center" | tools
-| align="center" | 2.3.1, 2.6.1, 2.7.1, 3.2.2
+| align="center" | 2.7.1, 3.2.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. Homepage: https://www.ruby-lang.org URL: https://www.ruby-lang.org Extensions: activesupport-5.2.8.1, addressable-2.8.4, arr-pm-0.0.12, backports-3.24.1, bundler-2.4.14, cabin-0.9.0, childprocess-4.1.0, clamp-1.3.2, concurrent-ruby-1.2.2, connection_pool-2.4.1, diff-lcs-1.5.0, ethon-0.16.0, faraday-1.2.0, faraday-net_http-3.0.2, faraday_middleware-1.2.0, ffi-1.15.5, gh-0.18.0, highline-2.1.0, i18n-1.14.1, json-2.6.3, launchy-2.5.2, minitest-5.18.0, multi_json-1.15.0, multipart-post-2.3.0, mustermann-3.0.0, net-http-persistent-2.9.4, net-http-pipeline-1.0.1, public_suffix-5.0.1, pusher-client-0.6.2, rack-2.2.4, rack-protection-3.0.6, rack-test-2.1.0, rspec-3.12.0, rspec-core-3.12.2, rspec-expectations-3.12.3, rspec-mocks-3.12.5, rspec-support-3.12.0, ruby2_keywords-0.0.5, sinatra-3.0.6, thread_safe-0.3.6, tilt-2.2.0, typhoeus-1.4.0, tzinfo-1.1.0, websocket-1.2.9, zeitwerk-2.6.8 Keyword:tools<br /><br /><br /></div>
-|-
-| align="center" | [https://rubygems.org rubygems]
-| align="center" | tools
-| align="center" | 2.3.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bundle which contains a collection of popular RubyGems, including ffi, childprocess, json, cabin, backports, arr-pm, clamp, multipart-post, faraday, faraday_middleware, highline, net-http-pipeline, net-http-persistent, multi_json, public_suffix, addressable, gh, launchy, ethon, typhoeus, websocket, pusher-client, diff-lcs, rspec-support, rspec-mocks, rspec-expections, rspec-core, rspec, rack, rack-protection, tilt, sinatra, rack-test, bundler. Homepage: https://rubygems.org Extensions: addressable-2.4.0, arr-pm-0.0.10, backports-3.6.8, bundler-1.15.4, cabin-0.9.0, childprocess-0.5.9, clamp-1.1.1, diff-lcs-1.2.5, ethon-0.10.1, faraday-0.10.0, faraday_middleware-0.10.1, ffi-1.9.14, gh-0.15.0, highline-1.7.8, json-2.0.2, launchy-2.4.3, multi_json-1.12.1, multipart-post-2.0.0, net-http-persistent-2.9.4, net-http-pipeline-1.0.1, public_suffix-2.0.4, pusher-client-0.6.2, rack-1.6.5, rack-protection-1.5.3, rack-test-0.6.3, rspec-3.5.0, rspec-core-3.5.4, rspec-expectations-3.5.0, rspec-mocks-3.5.0, rspec-support-3.5.0, sinatra-1.4.7, tilt-2.0.5, typhoeus-0.6.9, websocket-1.2.3 Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://www.rust-lang.org rust]
 | align="center" | tools
-| align="center" | 1.28.0, 1.41.0, 1.47.0, 1.53.0, 1.59.0, 1.65.0, 1.70.0, 1.76.0
+| align="center" | 1.47.0, 1.53.0, 1.59.0, 1.65.0, 1.70.0, 1.76.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. Homepage: https://www.rust-lang.org URL: https://www.rust-lang.org Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 4,647: / Line 3,992: @@
 | align="center" | [http://www.sagemath.org/ sagemath]
 | align="center" | tools
-| align="center" | 8.1, 9.1, 9.3
+| align="center" | 9.1, 9.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers. Homepage: http://www.sagemath.org/ URL: http://www.sagemath.org/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/COMBINE-lab/salmon salmon]
 | align="center" | bio
-| align="center" | 0.11.3, 0.12.0, 0.14.0, 0.14.2-1, 1.1.0, 1.3.0, 1.4.0, 1.10.2
+| align="center" | 1.3.0, 1.4.0, 1.10.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Homepage: https://github.com/COMBINE-lab/salmon URL: https://github.com/COMBINE-lab/salmon Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 4,662: / Line 4,007: @@
 | align="center" | [https://lomereiter.github.io/sambamba/ sambamba]
 | align="center" | bio
-| align="center" | 0.6.7, 0.7.1, 0.8.0
+| align="center" | 0.8.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth. Homepage: https://lomereiter.github.io/sambamba/ URL: https://lomereiter.github.io/sambamba/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/GregoryFaust/samblaster samblaster]
 | align="center" | bio
-| align="center" | 0.1.24, 0.1.26
+| align="center" | 0.1.26
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: samblaster: a tool to mark duplicates and extract discordant and split reads from sam files Homepage: https://github.com/GregoryFaust/samblaster URL: https://github.com/GregoryFaust/samblaster Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 4,677: / Line 4,022: @@
 | align="center" | [https://www.htslib.org/ samtools]
 | align="center" | bio
-| align="center" | 0.1.20, 1.3.1, 1.9, 1.10, 1.11, 1.12, 1.13, 1.15.1, 1.16.1, 1.17, 1.18, 1.20
+| align="center" | 0.1.20, 1.10, 1.11, 1.12, 1.13, 1.15.1, 1.16.1, 1.17, 1.18, 1.20
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Homepage: https://www.htslib.org/ URL: https://www.htslib.org/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 4,687: / Line 4,032: @@
 | align="center" | [http://www.scala-sbt.org/ sbt]
 | align="center" | tools
-| align="center" | 1.1.1, 1.3.13
+| align="center" | 1.3.13
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: sbt is a build tool for Scala, Java, and more. It requires Java 1.8 or later. sbt uses a small number of concepts to support flexible and powerful build definitions. There are not that many concepts, but sbt is not exactly like other build systems and there are details you will stumble on if you haven t read the documentation. The Getting Started Guide covers the concepts you need to know to create and maintain an sbt build definition. It is highly recommended to read the Getting Started Guide. Homepage: http://www.scala-sbt.org/ URL: http://www.scala-sbt.org/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://www.netlib.org/scalapack/ scalapack]
 | align="center" | math
-| align="center" | 2.0.2, 2.1.0, 2.2.0
+| align="center" | 2.1.0, 2.2.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. Homepage: https://www.netlib.org/scalapack/ URL: https://www.netlib.org/scalapack/ Keyword:math<br /><br /><br /></div>
 |-
@@ Line 4,707: / Line 4,052: @@
 | align="center" | [http://python.org/ scipy-stack]
 | align="center" | math
-| align="center" | 2017b, 2018b, 2019a, 2019b, 2020a, 2020b, 2021a, 2022a, 2023a, 2023b, 2024a
+| align="center" | 2020a, 2020b, 2021a, 2022a, 2023a, 2023b, 2024a
 | Documentation: [[Python]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bundle which contains the Scientific Python stack, including Cycler, mpmath, numpy, scipy, sympy, pandas, matplotlib, ipython_genutils, traitlets, ptyprocess, pathlib2, pickleshare, pexpect, simplegeneric, ipython, ipykernel, jupyter_client, jupyter_core, pyzmq, tornado, futures and ipyparallel. Homepage: http://python.org/ URL: http://python.org/ Compatible modules: python/3.10, python/3.11, python/3.12 Extensions: contourpy-1.2.1, cycler-0.12.1, fonttools-4.53.0, kiwisolver-1.4.5, matplotlib-3.9.0, mpmath-1.3.0, numpy-1.26.4, packaging-24.1, pandas-2.2.1, pillow-10.3.0, pyparsing-3.1.2, python_dateutil-2.9.0.post0, pytz-2024.1, scipy-1.13.1, six-1.16.0, sympy-1.12.1, tzdata-2024.1 Keyword:math<br /><br /><br /></div>
 |-
@@ Line 4,717: / Line 4,062: @@
 | align="center" | [https://www.labri.fr/perso/pelegrin/scotch/ scotch]
 | align="center" | math
-| align="center" | 6.0.4, 6.0.6, 6.0.9, 7.0.3
+| align="center" | 6.0.9, 7.0.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. Homepage: https://www.labri.fr/perso/pelegrin/scotch/ URL: https://www.labri.fr/perso/pelegrin/scotch/ Keyword:math<br /><br /><br /></div>
 |-
@@ Line 4,729: / Line 4,074: @@
 | align="center" | 0.994
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in picking out 3'-end adapters, which often include poor quality bases. Homepage: https://github.com/ucdavis-bioinformatics/scythe URL: https://github.com/ucdavis-bioinformatics/scythe<br /><br /><br /></div>
-|-
-| align="center" | [http://www.libsdl.org/ sdl]
-| align="center" | tools
-| align="center" | 1.2.15
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SDL: Simple DirectMedia Layer, a cross-platform multimedia library Homepage: http://www.libsdl.org/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [http://www.libsdl.org/ sdl2]
 | align="center" | tools
-| align="center" | 2.0.7, 2.0.10, 2.0.16
+| align="center" | 2.0.16
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SDL: Simple DirectMedia Layer, a cross-platform multimedia library Homepage: http://www.libsdl.org/ URL: http://www.libsdl.org/ Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 4,744: / Line 4,084: @@
 | align="center" | 2.1.1-20191211
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing succinct data structures. Homepage: https://github.com/simongog/sdsl-lite URL: https://github.com/simongog/sdsl-lite<br /><br /><br /></div>
-|-
-| align="center" | [https://www.disneyanimation.com/technology/seexpr.html seexpr]
-| align="center" | vis
-| align="center" | 2.11
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SeExpr is a simple expression language that we use to provide artistic control and customization to our core software. We use it for procedural geometry synthesis, image synthesis, simulation control, and much more. Homepage: https://www.disneyanimation.com/technology/seexpr.html Keyword:vis<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/szpiech/selscan selscan]
-| align="center" | bio
-| align="center" | 1.2.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: selscan -- a program to calculate EHH-based scans for positive selection in genomes selscan currently implements EHH, iHS, XP-EHH, nSL, and iHH12 and requires phased data. It should be run separately for each chromosome and population (or population pair for XP-EHH). selscan is 'dumb' with respect ancestral/derived coding and simply expects haplotype data to be coded 0/1. Unstandardized iHS scores are thus reported as ln(iHH1/iHH0) based on the coding you have provided. Homepage: https://github.com/szpiech/selscan Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://www.seqan.de/ seqan-library]
 | align="center" | -
-| align="center" | 1.4.2, 2.4.0
+| align="center" | 2.4.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data Homepage: https://www.seqan.de/ URL: https://www.seqan.de/<br /><br /><br /></div>
 |-
@@ Line 4,769: / Line 4,099: @@
 | align="center" | 1.2.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C++ interface to HTSlib, BWA-MEM and Fermi. Homepage: https://github.com/walaj/SeqLib URL: https://github.com/walaj/SeqLib<br /><br /><br /></div>
-|-
-| align="center" | [http://seqmule.openbioinformatics.org/en/latest/ seqmule]
-| align="center" | bio
-| align="center" | 1.2.6
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file. SeqMule also has some built-in functions, such as pooling consensus calls from various callers, plotting a Venn diagram showing intersection among different callers, and downloading databases. SeqMule can be used for both Mendelian disease study and cancer genome study. Homepage: http://seqmule.openbioinformatics.org/en/latest/ Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/lh3/seqtk/ seqtk]
-| align="center" | bio
-| align="center" | 1.2, 1.3
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Homepage: https://github.com/lh3/seqtk/ URL: https://github.com/lh3/seqtk/ Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [https://www.google.ca/search?q=sextractor sextractor]
-| align="center" | phys
-| align="center" | 2.19.5
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SExtractor is a program that builds a catalogue of objects from an astronomical image. Although it is particularly oriented towards reduction of large scale galaxy-survey data, it can perform reasonably well on moderately crowded star fields. Homepage: ://www.astromatic.net/software/sextractor Keyword:phys<br /><br /><br /></div>
 |-
 | align="center" | [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html shapeit]
@@ Line 4,809: / Line 4,124: @@
 | align="center" | 1.1.1, 1.5.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ShengBTE is a software package for solving the Boltzmann Transport Equation for phonons. Also installed is the 'thirdorder' package of Python scripts. Homepage: http://www.shengbte.org/ URL: http://www.shengbte.org/ Extensions: thirdorder-1.1.1 Keyword:phys<br /><br /><br /></div>
-|-
-| align="center" | [http://compbio.cs.toronto.edu/shrimp/ shrimp]
-| align="center" | -
-| align="center" | 2.2.3
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SHRiMP is a software package for aligning genomic reads against a target genome. It was primarily developed with the multitudinous short reads of next generation sequencing machines in mind, as well as Applied Biosystem's colourspace genomic representation. Homepage: http://compbio.cs.toronto.edu/shrimp/<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/jonathonl/shrinkwrap shrinkwrap]
@@ Line 4,828: / Line 4,138: @@
 | align="center" | bio
 | align="center" | 1.33
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Windowed Adaptive Trimming for fastq files using quality Homepage: https://github.com/najoshi/sickle Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Windowed Adaptive Trimming for fastq files using quality Homepage: https://github.com/najoshi/sickle URL: https://github.com/najoshi/sickle Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://departments.icmab.es/leem/siesta siesta]
 | align="center" | chem
-| align="center" | 4.1-MaX-3.0, 4.0.1, 4.1-b3, 4.1-b4, 4.1.5
+| align="center" | 4.1-MaX-3.0, 4.0.1, 4.1-b4, 4.1.5
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. Homepage: http://departments.icmab.es/leem/siesta URL: http://departments.icmab.es/leem/siesta Keyword:chem<br /><br /><br /></div>
-|-
-| align="center" | [http://sift.bii.a-star.edu.sg/ sift4g]
-| align="center" | bio
-| align="center" | 2.0.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SIFT predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. Homepage: http://sift.bii.a-star.edu.sg/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp signalp]
@@ Line 4,869: / Line 4,174: @@
 | align="center" | 0.7.0, 1.0.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: reimplementation of the DFT-D3 program Homepage: https://github.com/dftd3/simple-dftd3 URL: https://github.com/dftd3/simple-dftd3<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/precimed/simu simu]
-| align="center" | -
-| align="center" | 0.9.4
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SIMU simulats a GWAS based on real genotype data. This tool is a extension of gcta --simu-qt and gcta --simu-cc functionality. Homepage: https://github.com/precimed/simu URL: https://github.com/precimed/simu<br /><br /><br /></div>
 |-
 | align="center" | [https://www.singular.uni-kl.de/ singular]
@@ Line 4,887: / Line 4,187: @@
 | align="center" | [https://slepc.upv.es/ slepc]
 | align="center" | -
-| align="center" | 3.10.2, 3.14.2, 3.17.2, 3.19.2, 3.20.1
+| align="center" | 3.14.2, 3.17.2, 3.19.2, 3.20.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. Homepage: https://slepc.upv.es/ URL: https://slepc.upv.es/ Compatible modules: python/3.11, python/3.10 Extensions: slepc4py-3.20.1<br /><br /><br /></div>
 |-
@@ Line 4,897: / Line 4,197: @@
 | align="center" | [https://www.slicer.org/ slicer]
 | align="center" | -
-| align="center" | 4.10.1, 4.11.20210226
+| align="center" | 4.11.20210226
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. Built over two decades through support from the National Institutes of Health and a worldwide developer community, Slicer brings free, powerful cross-platform processing tools to physicians, researchers, and the general public. Homepage: https://www.slicer.org/ URL: https://www.slicer.org/<br /><br /><br /></div>
 |-
 | align="center" | [https://messerlab.org/slim slim]
 | align="center" | -
-| align="center" | 3.3.2, 3.4.0, 4.0.1
+| align="center" | 3.4.0, 4.0.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Homepage: https://messerlab.org/slim URL: https://messerlab.org/slim<br /><br /><br /></div>
 |-
@@ Line 4,918: / Line 4,218: @@
 | align="center" | -
 | align="center" | 13.1.0.221970
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PacBios open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. You can analyze, visualize, and manage your data through an intuitive GUI or command-line interface. You can also integrate SMRT Analysis in your existing data workflow through the extensive set of APIs provided Homepage: https://www.pacb.com/support/software-downloads/ URL: https://www.pacb.com/support/software-downloads/<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PacBio's open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. You can analyze, visualize, and manage your data through an intuitive GUI or command-line interface. You can also integrate SMRT Analysis in your existing data workflow through the extensive set of APIs provided Homepage: https://www.pacb.com/support/software-downloads/ URL: https://www.pacb.com/support/software-downloads/<br /><br /><br /></div>
 |-
 | align="center" | [http://korflab.ucdavis.edu/software.html snap]
@@ Line 4,927: / Line 4,227: @@
 | align="center" | [https://github.com/google/snappy snappy]
 | align="center" | tools
-| align="center" | 1.1.3, 1.1.8
+| align="center" | 1.1.8
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression. Homepage: https://github.com/google/snappy URL: https://github.com/google/snappy Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 4,942: / Line 4,242: @@
 | align="center" | [https://pcingola.github.io/SnpEff/ snpeff]
 | align="center" | bio
-| align="center" | 4.3t, 5.0
+| align="center" | 5.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). Homepage: https://pcingola.github.io/SnpEff/ URL: https://pcingola.github.io/SnpEff/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 4,952: / Line 4,252: @@
 | align="center" | [http://soap.genomics.org.cn/index.html soapdenovo2]
 | align="center" | bio
-| align="center" | r240, r242
+| align="center" | r242
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo. Homepage: http://soap.genomics.org.cn/index.html URL: http://soap.genomics.org.cn/index.html Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 4,962: / Line 4,262: @@
 | align="center" | [http://bioinfo.lifl.fr/RNA/sortmerna/ sortmerna]
 | align="center" | bio
-| align="center" | 2.1, 4.2.0, 4.3.4, 4.3.6
+| align="center" | 4.2.0, 4.3.4, 4.3.6
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Homepage: http://bioinfo.lifl.fr/RNA/sortmerna/ URL: http://bioinfo.lifl.fr/RNA/sortmerna/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://cab.spbu.ru/software/spades/ spades]
 | align="center" | bio
-| align="center" | 3.11.1, 3.13.0, 3.13.1, 3.14.1, 3.15.1, 3.15.3, 3.15.4
+| align="center" | 3.14.1, 3.15.1, 3.15.3, 3.15.4
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Genome assembler for single-cell and isolates data sets Homepage: http://cab.spbu.ru/software/spades/ URL: http://cab.spbu.ru/software/spades/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://spark.apache.org spark]
 | align="center" | tools
-| align="center" | 2.1.0, 2.1.1, 2.2.0, 2.2.1, 2.3.0, 2.4.4, 3.0.0, 3.3.0
+| align="center" | 3.0.0, 3.3.0
 | Documentation: [[Apache Spark]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Spark is Hadoop MapReduce done in memory Homepage: http://spark.apache.org URL: http://spark.apache.org Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 4,992: / Line 4,292: @@
 | align="center" | [https://github.com/spglib/spglib spglib]
 | align="center" | chem
-| align="center" | 1.9.9, 1.16.0, 2.0.2
+| align="center" | 1.16.0, 2.0.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Spglib is a C library for finding and handling crystal symmetries. Homepage: https://github.com/spglib/spglib URL: https://github.com/spglib/spglib Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 5,003: / Line 4,303: @@
 | align="center" | math
 | align="center" | 5.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Scalable Parallel Pseudo Random Number Generators Library Homepage: http://www.sprng.org/ Keyword:math<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Scalable Parallel Pseudo Random Number Generators Library Homepage: http://www.sprng.org/ URL: http://www.sprng.org/ Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [https://www.sqlite.org/ sqlite]
@@ Line 5,009: / Line 4,309: @@
 | align="center" | 3.38.5, 3.43.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SQLite: SQL Database Engine in a C Library Homepage: https://www.sqlite.org/ URL: https://www.sqlite.org/<br /><br /><br /></div>
-|-
-| align="center" | [http://eddylab.org/software.html squid]
-| align="center" | bio
-| align="center" | 1.9g
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Author: Sean Eddy A C library that is bundled with much of the above software. C function library for sequence analysis. SQUID is my own personal library of C functions and utility programs for sequence analysis. I don't really suggest that you use it in your programs, as I change it at will. However, it does contains some small utility programs that some people have found useful in scripts that drive large HMMER tasks. Homepage: http://eddylab.org/software.html Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/ncbi/sra-tools sra-toolkit]
 | align="center" | bio
-| align="center" | 2.8.2-1, 2.9.6, 2.10.8, 3.0.0, 3.0.9
+| align="center" | 2.10.8, 3.0.0, 3.0.9
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format Homepage: https://github.com/ncbi/sra-tools URL: https://github.com/ncbi/sra-tools Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 5,024: / Line 4,319: @@
 | align="center" | 3.1.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Single Read Paired Read Indel Substitution Minimizer Homepage: https://github.com/ncbi/SRPRISM URL: https://github.com/ncbi/SRPRISM<br /><br /><br /></div>
-|-
-| align="center" | [https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE-longread sspace-longread]
-| align="center" | bio
-| align="center" | 1-1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SSPACE-LongRead is a stand-alone program for scaffolding pre-assembled contigs using long reads (e.g. PacBio RS reads). Homepage: https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE-longread Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/nsoranzo/sspace_basic sspace_basic]
-| align="center" | bio
-| align="center" | 2.1.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension Homepage: https://github.com/nsoranzo/sspace_basic Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library ssw]
@@ Line 5,042: / Line 4,327: @@
 | align="center" | [http://creskolab.uoregon.edu/stacks/ stacks]
 | align="center" | bio
-| align="center" | 2.3e, 1.46, 2.53, 2.55, 2.57, 2.59, 2.60, 2.62, 2.64
+| align="center" | 2.53, 2.55, 2.57, 2.59, 2.60, 2.62, 2.64
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. Homepage: http://creskolab.uoregon.edu/stacks/ URL: http://creskolab.uoregon.edu/stacks/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/alexdobin/STAR star]
 | align="center" | bio
-| align="center" | 2.6.1c, 2.7.0a, 2.7.1a, 2.7.3a, 2.7.4a, 2.7.5a, 2.7.8a, 2.7.9a, 2.7.11a, 2.7.11b
+| align="center" | 2.7.5a, 2.7.8a, 2.7.9a, 2.7.11a, 2.7.11b
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. Homepage: https://github.com/alexdobin/STAR URL: https://github.com/alexdobin/STAR Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 5,057: / Line 4,342: @@
 | align="center" | [http://mdx.plm.automation.siemens.com/star-ccm-plus starccm]
 | align="center" | phys
-| align="center" | 11.06.011-R8, 12.04.011-R8, 12.06.011-R8, 13.04.010-R8, 13.06.012-R8, 14.02.012-R8, 14.04.013-R8, 14.06.013-R8, 15.04.010-R8, 16.02.008-R8, 16.02.009-R8, 16.04.007-R8, 16.04.012-R8, 16.06.008-R8, 17.02.007-R8, 17.02.008-R8, 17.04.007-R8, 17.04.008-R8, 17.06.007-R8, 17.06.008-R8, 18.02.008-R8, 18.04.008-R8, 18.06.006-R8, 19.04.007-R8
+| align="center" | 15.04.010-R8, 16.02.008-R8, 16.02.009-R8, 16.04.007-R8, 16.04.012-R8, 16.06.008-R8, 17.02.007-R8, 17.02.008-R8, 17.04.007-R8, 17.04.008-R8, 17.06.007-R8, 17.06.008-R8, 18.02.008-R8, 18.04.008-R8, 18.06.006-R8, 19.04.007-R8
 | Documentation: [[StarCCM]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Predicting the real-world performance of a product requires simulation tools that span a variety of engineering disciplines. STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface. This version uses double precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus URL: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys<br /><br /><br /></div>
 |-
 | align="center" | [http://mdx.plm.automation.siemens.com/star-ccm-plus starccm-mixed]
 | align="center" | phys
-| align="center" | 11.06.011, 12.04.011, 12.06.011, 13.04.010, 13.06.012, 14.02.012, 14.04.013, 14.06.013, 15.04.010, 16.02.008, 16.02.009, 16.04.007, 16.04.012, 16.06.008, 17.02.007, 17.02.008, 17.04.007, 17.04.008, 17.06.007, 17.06.008, 18.02.008, 18.04.008, 18.06.006, 19.04.007
+| align="center" | 15.04.010, 16.02.008, 16.02.009, 16.04.007, 16.04.012, 16.06.008, 17.02.007, 17.02.008, 17.04.007, 17.04.008, 17.06.007, 17.06.008, 18.02.008, 18.04.008, 18.06.006, 19.04.007
 | Documentation: [[StarCCM]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Predicting the real-world performance of a product requires simulation tools that span a variety of engineering disciplines. STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface. This version uses mixed precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus URL: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys<br /><br /><br /></div>
 |-
@@ Line 5,069: / Line 4,354: @@
 | align="center" | 0.34
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Perl interface with the R statistical program Homepage: https://metacpan.org/pod/Statistics::R URL: https://metacpan.org/pod/Statistics::R<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/Illumina/strelka strelka]
-| align="center" | -
-| align="center" | 2.9.10
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs. Homepage: https://github.com/Illumina/strelka URL: https://github.com/Illumina/strelka<br /><br /><br /></div>
 |-
 | align="center" | [https://ccb.jhu.edu/software/stringtie/ stringtie]
 | align="center" | bio
-| align="center" | 1.3.4d, 2.0, 2.1.0, 2.1.3, 2.1.5, 2.2.1
+| align="center" | 2.1.3, 2.1.5, 2.2.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts Homepage: https://ccb.jhu.edu/software/stringtie/ URL: https://ccb.jhu.edu/software/stringtie/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 5,087: / Line 4,367: @@
 | align="center" | [http://su2.stanford.edu su2]
 | align="center" | math
-| align="center" | 5.0.0, 6.0.1, 6.1.0, 6.2.0, 7.0.0, 7.0.5, 7.0.8, 7.5.1
+| align="center" | 7.0.8, 7.5.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An open-source collection of software tools written in C++ for performing Partial Differential Equation (PDE) analysis and solving PDE-constrained optimization problems. The toolset is designed with computational fluid dynamics and aerodynamic shape optimization in mind. Homepage: http://su2.stanford.edu URL: http://su2.stanford.edu Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [http://subread.sourceforge.net/ subread]
 | align="center" | bio
-| align="center" | 1.5.2, 1.6.4, 2.0.0, 2.0.3, 2.0.6
+| align="center" | 2.0.3, 2.0.6
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: High performance read alignment, quantification and mutation discovery Homepage: http://subread.sourceforge.net/ URL: http://subread.sourceforge.net/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://faculty.cse.tamu.edu/davis/suitesparse.html suitesparse]
 | align="center" | math
-| align="center" | 4.5.4, 5.4.0, 5.7.1, 5.10.1, 5.13.0, 7.6.0
+| align="center" | 5.7.1, 5.10.1, 5.13.0, 7.6.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SuiteSparse is a collection of libraries to manipulate sparse matrices. Homepage: https://faculty.cse.tamu.edu/davis/suitesparse.html URL: https://faculty.cse.tamu.edu/davis/suitesparse.html Keyword:math<br /><br /><br /></div>
 |-
-| align="center" | [http://metabarcoding.org/sumatra sumaclust]
+| align="center" | [https://github.com/eclipse/sumo/ sumo]
+| align="center" | -
+| align="center" | 1.7.0, 1.9.0, 1.9.2, 1.15.0
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Eclipse Sumo is an open source, highly portable, microscopic and continuous traffic simulation package designed to handle large road networks. Homepage: https://github.com/eclipse/sumo/ URL: https://github.com/eclipse/sumo/ Compatible modules: python/3.8, python/3.9, python/3.10<br /><br /><br /></div>
+|-
+| align="center" | [https://computing.llnl.gov/projects/sundials sundials]
+| align="center" | -
+| align="center" | 2.7.0, 5.3.0, 5.7.0, 6.4.1, 6.6.0
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers Homepage: https://computing.llnl.gov/projects/sundials URL: https://computing.llnl.gov/projects/sundials<br /><br /><br /></div>
+|-
+| align="center" | [http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ superlu]
+| align="center" | math
+| align="center" | 5.2.1
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. Homepage: http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ URL: http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ Keyword:math<br /><br /><br /></div>
+|-
+| align="center" | [https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome supernova]
 | align="center" | bio
-| align="center" | 1.0.20
+| align="center" | 2.1.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences. Homepage: http://metabarcoding.org/sumatra Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [https://github.com/eclipse/sumo/ sumo]
-| align="center" | -
-| align="center" | 1.7.0, 1.9.0, 1.9.2, 1.15.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Eclipse Sumo is an open source, highly portable, microscopic and continuous traffic simulation package designed to handle large road networks. Homepage: https://github.com/eclipse/sumo/ URL: https://github.com/eclipse/sumo/ Compatible modules: python/3.8, python/3.9, python/3.10<br /><br /><br /></div>
-|-
-| align="center" | [https://computing.llnl.gov/projects/sundials sundials]
-| align="center" | -
-| align="center" | 2.7.0, 4.1.0, 5.3.0, 5.7.0, 6.4.1, 6.6.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers Homepage: https://computing.llnl.gov/projects/sundials URL: https://computing.llnl.gov/projects/sundials<br /><br /><br /></div>
-|-
-| align="center" | [http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ superlu]
-| align="center" | math
-| align="center" | 5.2.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. Homepage: http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ URL: http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ Keyword:math<br /><br /><br /></div>
-|-
-| align="center" | [https://www.google.ca/search?q=superlu_dist superlu_dist]
-| align="center" | -
-| align="center" | 6.1.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SuperLU_DIST contains a set of subroutines to solve a sparse linear system A*X=B. It uses Gaussian elimination with static pivoting (GESP). Homepage:<br /><br /><br /></div>
-|-
-| align="center" | [https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome supernova]
-| align="center" | bio
-| align="center" | 2.0.0, 2.1.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Supernova is delivered as a single, self-contained tar file that can be unpacked anywhere on your system. It bundles all of its own required software dependencies, which are pre-compiled to run on a range of Linux distributions. Homepage: https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome URL: https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 5,152: / Line 4,422: @@
 | align="center" | [http://www.swig.org/ swig]
 | align="center" | -
-| align="center" | 3.0.12, 4.0.1, 4.0.2, 4.1.1
+| align="center" | 4.0.1, 4.0.2, 4.1.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. Homepage: http://www.swig.org/ URL: http://www.swig.org/<br /><br /><br /></div>
 |-
@@ Line 5,172: / Line 4,442: @@
 | align="center" | [http://tau.uoregon.edu tau]
 | align="center" | tools
-| align="center" | 2.27.1, 2.30.1
+| align="center" | 2.30.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The TAU Performance System is a portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python. Homepage: http://tau.uoregon.edu URL: http://tau.uoregon.edu Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 5,187: / Line 4,457: @@
 | align="center" | [https://github.com/oneapi-src/oneTBB tbb]
 | align="center" | tools
-| align="center" | 2018_U5, 2017.2.132, 2020.2, 2021.8.0, 2021.10.0
+| align="center" | 2020.2, 2021.8.0, 2021.10.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability. Homepage: https://github.com/oneapi-src/oneTBB URL: https://github.com/oneapi-src/oneTBB Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 5,199: / Line 4,469: @@
 | align="center" | 0.3.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Light-weight tight-binding framework Homepage: https://github.com/tblite/tblite URL: https://github.com/tblite/tblite Compatible modules: python/3.10, python/3.11 Extensions: tblite-0.3.0<br /><br /><br /></div>
-|-
-| align="center" | [http://www.tcl.tk/ tcl]
-| align="center" | tools
-| align="center" | 8.5.19, 8.6.8
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. Homepage: http://www.tcl.tk/ Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://developer.nvidia.com/tensorrt tensorrt]
 | align="center" | -
-| align="center" | 6.0.1.5, 8.6.1.6
+| align="center" | 8.6.1.6
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NVIDIA TensorRT is a platform for high-performance deep learning inference Homepage: https://developer.nvidia.com/tensorrt URL: https://developer.nvidia.com/tensorrt Compatible modules: python/3.10, python/3.11<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NVIDIA TensorRT is a platform for high-performance deep learning inference Homepage: https://developer.nvidia.com/tensorrt URL: https://developer.nvidia.com/tensorrt Compatible modules: python/3.8, python/3.9, python/3.10, python/3.11<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/tesseract-ocr/tesseract tesseract]
@@ Line 5,219: / Line 4,484: @@
 | align="center" | 0.13.0, 0.14.2, 0.16.0, 0.18.1, 0.19.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Apache Thrift software framework, for scalable cross-language services development, combines a software stack with a code generation engine to build services that work efficiently and seamlessly between C++, Java, Python, PHP, Ruby, Erlang, Perl, Haskell, C#, Cocoa, JavaScript, Node.js, Smalltalk, OCaml and Delphi and other languages. Homepage: https://thrift.apache.org/ URL: https://thrift.apache.org/ Compatible modules: python/3.10, python/3.11<br /><br /><br /></div>
-|-
-| align="center" | [http://wiki.tcl.tk/1877 tktable]
-| align="center" | tools
-| align="center" | 2.10
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Tcl is a simple-to-learn yet very powerful language. Its syntax is described in just a dozen rules, but it has all the features needed to rapidly create useful programs in almost any field of application - on a wide variety of international platforms. Tk is a graphical toolkit for Tcl. It allows you to develop graphical applications that run on Windows, Linux, MacOS X and many other platforms. And not just from Tcl - Tk can be used from many languages including C, Ruby, Perl, Python and Lua. Homepage: http://wiki.tcl.tk/1877 Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm tmhmm]
 | align="center" | bio
 | align="center" | 2.0c
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: TMHMM 2.0 predicts transmembrane helices in proteins. The method is described in: Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes. Anders Krogh and Bjorn Larsson, Gunnar von Heijne, and Erik L.L. Sonnhammer. J. Mol. Biol. 305:567-580, 2001. and: A hidden Markov model for predicting transmembrane helices in protein sequences. Erik L.L. Sonnhammer, Gunnar von Heijne, and Anders Krogh. In J. Glasgow et al., eds.: Proc. of ISMB6, pages 175-182. AAAI Press, 1998. Homepage: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: TMHMM 2.0 predicts transmembrane helices in proteins. The method is described in: Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes. Anders Krogh and Bjorn Larsson, Gunnar von Heijne, and Erik L.L. Sonnhammer. J. Mol. Biol. 305:567-580, 2001. and: A hidden Markov model for predicting transmembrane helices in protein sequences. Erik L.L. Sonnhammer, Gunnar von Heijne, and Anders Krogh. In J. Glasgow et al., eds.: Proc. of ISMB6, pages 175-182. AAAI Press, 1998. Homepage: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm URL: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://sourceforge.net/projects/togl/ togl]
@@ Line 5,237: / Line 4,497: @@
 | align="center" | [http://ccb.jhu.edu/software/tophat/ tophat]
 | align="center" | bio
-| align="center" | 2.1.1, 2.1.2
+| align="center" | 2.1.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: TopHat is a fast splice junction mapper for RNA-Seq reads. Homepage: http://ccb.jhu.edu/software/tophat/ URL: http://ccb.jhu.edu/software/tophat/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://towhee.sourceforge.net/ towhee]
 | align="center" | chem
-| align="center" | 8.1.0, 8.2.3
+| align="center" | 8.2.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling. The code has subsequently been extended to several ensembles, many different force fields, and solid (or at least porous) phases. Homepage: http://towhee.sourceforge.net/ URL: http://towhee.sourceforge.net/ Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 5,253: / Line 4,513: @@
 | align="center" | bio
 | align="center" | 2.0.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: de novo assembly of RNA-Seq data using ABySS Homepage: http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/ Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: de novo assembly of RNA-Seq data using ABySS Homepage: http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/ URL: http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://transdecoder.github.io/ transdecoder]
 | align="center" | bio
-| align="center" | 3.0.1, 5.5.0, 5.7.1
+| align="center" | 5.5.0, 5.7.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Homepage: https://transdecoder.github.io/ URL: https://transdecoder.github.io/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 5,277: / Line 4,537: @@
 | align="center" | [https://tandem.bu.edu/trf/trf.html trf]
 | align="center" | bio
-| align="center" | 4.09, 4.09.1
+| align="center" | 4.09.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A tandem repeat in DNA is two or more adjacent, approximate copies of a pattern of nucleotides. Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. In order to use the program, the user submits a sequence in FASTA format. There is no need to specify the pattern, the size of the pattern or any other parameter. The output consists of two files: a repeat table file and an alignment file. The repeat table, viewable in a web browser, contains information about each repeat, including its location, size, number of copies and nucleotide content. Clicking on the location indices for one of the table entries opens a second browser page that shows an alignment of the copies against a consensus pattern. The program is very fast, analyzing sequences on the order of .5Mb in just a few seconds. Submitted sequences may be of arbitrary length. Repeats with pattern size in the range from 1 to 2000 bases are detected. Homepage: https://tandem.bu.edu/trf/trf.html URL: https://tandem.bu.edu/trf/trf.html Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://trilinos.org trilinos]
 | align="center" | tools
-| align="center" | 12.10.1, 12.12.1, 13.0.1, 13.2.0, 13.4.0, 13.4.1, 15.1.1
+| align="center" | 13.0.1, 13.2.0, 13.4.0, 13.4.1, 15.1.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages. Homepage: https://trilinos.org URL: https://trilinos.org Compatible modules: python/3.11 Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 5,288: / Line 4,548: @@
 | align="center" | bio
 | align="center" | 1.4
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment Homepage: http://trimal.cgenomics.org/ Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment Homepage: http://trimal.cgenomics.org/ URL: http://trimal.cgenomics.org/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://www.usadellab.org/cms/?page=trimmomatic trimmomatic]
 | align="center" | bio
-| align="center" | 0.36, 0.39
+| align="center" | 0.39
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line. Homepage: http://www.usadellab.org/cms/?page=trimmomatic URL: http://www.usadellab.org/cms/?page=trimmomatic Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://trinityrnaseq.github.io/ trinity]
 | align="center" | bio
-| align="center" | 2.8.4, 2.8.5, 2.9.0, 2.11.0, 2.12.0, 2.13.2, 2.14.0
+| align="center" | 2.11.0, 2.12.0, 2.13.2, 2.14.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. Homepage: http://trinityrnaseq.github.io/ URL: http://trinityrnaseq.github.io/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [https://trinotate.github.io/ trinotate]
 | align="center" | bio
-| align="center" | 3.0.2, 3.2.0, 3.2.1, 3.2.2, 4.0.0
+| align="center" | 3.2.1, 3.2.2, 4.0.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Homepage: https://trinotate.github.io/ URL: https://trinotate.github.io/ Extensions: CGI-4.57, Text::NSP-1.31 Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 5,312: / Line 4,572: @@
 | align="center" | [http://lowelab.ucsc.edu/ trnascan-se]
 | align="center" | bio
-| align="center" | 2.0.0, 2.0.7, 2.0.12
+| align="center" | 2.0.7, 2.0.12
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: tRNAscan-SE: An improved tool for transfer RNA detection, Patricia Chan and Todd Lowe, School of Engineering, University of California, Santa Cruz, CA. tRNAscan-SE was written in the PERL (version 5.0) script language. Input consists of DNA or RNA sequences in FASTA format. tRNA predictions are output in standard tabular or ACeDB format. tRNAscan-SE does no tRNA detection itself, but instead combines the strengths of three independent tRNA prediction programs by negotiating the flow of information between them, performing a limited amount of post-processing, and outputting the results in one of several formats. Homepage: http://lowelab.ucsc.edu/ URL: http://lowelab.ucsc.edu/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 5,327: / Line 4,587: @@
 | align="center" | [https://www.openucx.org/ ucx]
 | align="center" | -
-| align="center" | 1.5.2, 1.6.0, 1.8.0, 1.9.0, 1.10.0, 1.12.1, 1.14.1, 1.16.0
+| align="center" | 1.8.0, 1.9.0, 1.10.0, 1.12.1, 1.14.1, 1.16.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Unified Communication X An open-source production grade communication framework for data centric and high-performance applications Homepage: https://www.openucx.org/ URL: https://www.openucx.org/<br /><br /><br /></div>
 |-
@@ Line 5,342: / Line 4,602: @@
 | align="center" | [https://www.unixodbc.org unixodbc]
 | align="center" | -
-| align="center" | 2.3.7, 2.3.9
+| align="center" | 2.3.9
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: unixODBC provides a uniform interface between application and database driver Homepage: https://www.unixodbc.org URL: https://www.unixodbc.org<br /><br /><br /></div>
 |-
 | align="center" | [https://valgrind.org valgrind-mpi]
 | align="center" | tools
-| align="center" | 3.14.0, 3.16.1, 3.21.0
+| align="center" | 3.16.1, 3.21.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Valgrind: Debugging and profiling tools Homepage: https://valgrind.org URL: https://valgrind.org Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/dkoboldt/varscan varscan]
 | align="center" | -
-| align="center" | 2.4.1, 2.4.2, 2.4.6
+| align="center" | 2.4.2, 2.4.6
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Variant calling and somatic mutation/CNV detection for next-generation sequencing data Homepage: https://github.com/dkoboldt/varscan URL: https://github.com/dkoboldt/varscan<br /><br /><br /></div>
 |-
@@ Line 5,359: / Line 4,619: @@
 | align="center" | 1.5.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PLATform for Assembling NUcleotide Sequences Homepage: http://platanus.bio.titech.ac.jp/ URL: http://platanus.bio.titech.ac.jp/<br /><br /><br /></div>
-|-
-| align="center" | [https://www.vaultproject.io/ vault]
-| align="center" | -
-| align="center" | 1.0.3
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Manage Secrets and Protect Sensitive Data Secure, store and tightly control access to tokens, passwords, certificates, encryption keys for protecting secrets and other sensitive data using a UI, CLI, or HTTP API. Homepage: https://www.vaultproject.io/<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/vcflib/vcflib vcflib]
@@ Line 5,372: / Line 4,627: @@
 | align="center" | [https://vcftools.github.io vcftools]
 | align="center" | bio
-| align="center" | 0.1.14, 0.1.16
+| align="center" | 0.1.16
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. Homepage: https://vcftools.github.io URL: https://vcftools.github.io Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 5,378: / Line 4,633: @@
 | align="center" | bio
 | align="center" | 1.2.10
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Sequence assembler for very short reads Homepage: http://www.ebi.ac.uk/~zerbino/velvet/ Keyword:bio<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Sequence assembler for very short reads Homepage: http://www.ebi.ac.uk/~zerbino/velvet/ URL: http://www.ebi.ac.uk/~zerbino/velvet/ Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://csg.sph.umich.edu/kang/verifyBamID/index.html verifybamid]
-| align="center" | bio
-| align="center" | 1.1.3
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples. verifyBamID can detect sample contamination and swaps when external genotypes are available. When external genotypes are not available, verifyBamID still robustly detects sample swaps. Homepage: http://csg.sph.umich.edu/kang/verifyBamID/index.html Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [http://viennacl.sourceforge.net/ viennacl]
-| align="center" | math
-| align="center" | 1.7.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ViennaCL is a free open-source linear algebra library for computations on many-core architectures (GPUs, MIC) and multi-core CPUs. The library is written in C++ and supports CUDA, OpenCL, and OpenMP (including switches at runtime). Homepage: http://viennacl.sourceforge.net/ Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [http://www.tbi.univie.ac.at/RNA/ viennarna]
 | align="center" | bio
-| align="center" | 2.4.9, 2.4.10, 2.4.11, 2.5.0, 2.5.1
+| align="center" | 2.5.0, 2.5.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. Homepage: http://www.tbi.univie.ac.at/RNA/ URL: http://www.tbi.univie.ac.at/RNA/ Compatible modules: python/3.8, python/3.9, python/3.10 Keyword:bio<br /><br /><br /></div>
-|-
-| align="center" | [https://plsuser.llnl.gov/bbs/vinalc/index.html vinalc]
-| align="center" | -
-| align="center" | 1.3.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A very popular PC-based molecular docking program, AutoDock Vina, was modified and parallelized, using an MPI and multithreading hybrid scheme, and potentially can be used in the future on exascale machines, without sacrificing accuracy. The resulting program scales up to more than 15K CPUs with a very low overhead cost. Homepage: https://plsuser.llnl.gov/bbs/vinalc/index.html URL: https://plsuser.llnl.gov/bbs/vinalc/index.html<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/simroux/VirSorter virsorter]
@@ Line 5,423: / Line 4,663: @@
 | align="center" | math
 | align="center" | 0.4.6
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles. Homepage: http://math.lbl.gov/voro++/ Keyword:math<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles. Homepage: http://math.lbl.gov/voro++/ URL: http://math.lbl.gov/voro++/ Keyword:math<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/torognes/vsearch vsearch]
 | align="center" | bio
-| align="center" | 2.5.0, 2.9.1, 2.13.3, 2.13.4, 2.15.2, 2.21.1
+| align="center" | 2.13.3, 2.13.4, 2.15.2, 2.21.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads. Homepage: https://github.com/torognes/vsearch URL: https://github.com/torognes/vsearch Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://www.vtk.org vtk]
 | align="center" | vis
-| align="center" | 6.3.0, 8.0.0, 8.1.1, 8.2.0, 9.0.1, 9.1.0, 9.3.0
+| align="center" | 8.2.0, 9.0.1, 9.1.0, 9.3.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. Homepage: http://www.vtk.org URL: http://www.vtk.org Compatible modules: python/3.11, python/3.10 Keyword:vis<br /><br /><br /></div>
 |-
 | align="center" | [http://www.vtk.org vtk-mpi]
 | align="center" | vis
-| align="center" | 6.3.0, 9.0.1, 9.0.3
+| align="center" | 9.0.1, 9.0.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. Homepage: http://www.vtk.org URL: http://www.vtk.org Compatible modules: python/3.8, python/3.7, python/3.6 Keyword:vis<br /><br /><br /></div>
 |-
 | align="center" | [https://software.intel.com/en-us/vtune vtune]
 | align="center" | tools
-| align="center" | 2018.3, 2019.3, 2020.1, 2022.2
+| align="center" | 2020.1, 2022.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java. Homepage: https://software.intel.com/en-us/vtune URL: https://software.intel.com/en-us/vtune Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 5,452: / Line 4,692: @@
 | align="center" | [http://www.wannier.org/ wannier90]
 | align="center" | chem
-| align="center" | 1.2, 3.0.0, 3.1.0
+| align="center" | 1.2, 3.1.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Maximally-Localised Generalised Wannier Functions calculates the counterpart of localized molecular orbitals for crystalline systems from the wavefuction. Homepage: http://www.wannier.org/ URL: http://www.wannier.org/ Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 5,472: / Line 4,712: @@
 | align="center" | [http://www.cpc.noaa.gov/products/wesley/wgrib2/ wgrib2]
 | align="center" | geo
-| align="center" | 2.0.7, 3.0.0
+| align="center" | 3.0.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A program to decode/manipulate GRIB-2 files. Homepage: http://www.cpc.noaa.gov/products/wesley/wgrib2/ URL: http://www.cpc.noaa.gov/products/wesley/wgrib2/ Keyword:geo<br /><br /><br /></div>
-|-
-| align="center" | [http://membrane.urmc.rochester.edu/content/wham wham]
-| align="center" | math
-| align="center" | 2.0.9.1
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: fast, memory efficient implementation of the Weighted Histogram Analysis Method (WHAM). Homepage: http://membrane.urmc.rochester.edu/content/wham Keyword:math<br /><br /><br /></div>
-|-
-| align="center" | [https://www.geometrictools.com/ wildmagic]
-| align="center" | -
-| align="center" | 5.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Geometric Tools Wild Magic is a C++ library for real-time computer graphics and physics, mathematics, geometry, numerical analysis, and image analysis. Homepage: https://www.geometrictools.com/ URL: https://www.geometrictools.com/<br /><br /><br /></div>
 |-
 | align="center" | [https://github.com/marbl/Winnowmap winnowmap]
@@ Line 5,492: / Line 4,722: @@
 | align="center" | [http://www.wrf-model.org wps]
 | align="center" | geo
-| align="center" | 3.9.1, 4.1, 4.2
+| align="center" | 4.1, 4.2
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. Homepage: http://www.wrf-model.org URL: http://www.wrf-model.org Keyword:geo<br /><br /><br /></div>
 |-
 | align="center" | [https://www.wrf-model.org wrf]
 | align="center" | geo
-| align="center" | 3.9.1.1, 4.1.3, 4.2.1, 4.3.3
+| align="center" | 4.1.3, 4.2.1, 4.3.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. Homepage: https://www.wrf-model.org URL: https://www.wrf-model.org Keyword:geo<br /><br /><br /></div>
 |-
@@ Line 5,503: / Line 4,733: @@
 | align="center" | -
 | align="center" | 2.5
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output Homepage: https://github.com/ruanjue/wtdbg2 URL: https://github.com/ruanjue/wtdbg2<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Homepage: https://github.com/ruanjue/wtdbg2 URL: https://github.com/ruanjue/wtdbg2<br /><br /><br /></div>
 |-
 | align="center" | [https://www.wxwidgets.org wxwidgets]
 | align="center" | tools
-| align="center" | 3.1.1, 3.1.4, 3.1.7
+| align="center" | 3.1.4, 3.1.7
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI. Homepage: https://www.wxwidgets.org URL: https://www.wxwidgets.org Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: wxPython-4.1.1 Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 5,527: / Line 4,757: @@
 | align="center" | [https://xerces.apache.org/xerces-c/ xerces-c++]
 | align="center" | tools
-| align="center" | 3.1.1, 3.2.2, 3.2.3
+| align="center" | 3.2.2, 3.2.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs. Homepage: https://xerces.apache.org/xerces-c/ URL: https://xerces.apache.org/xerces-c/ Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 5,542: / Line 4,772: @@
 | align="center" | [https://github.com/grimme-lab/xtb xtb]
 | align="center" | chem
-| align="center" | 6.3.0, 6.3.3, 6.4.0, 6.4.1, 6.5.0, 6.5.1, 6.6.1
+| align="center" | 6.3.3, 6.4.0, 6.4.1, 6.5.0, 6.5.1, 6.6.1
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: xtb - Extended tight-binding semi-empirical quantum mechanics Homepage: https://github.com/grimme-lab/xtb URL: https://github.com/grimme-lab/xtb Compatible modules: python/3.10, python/3.11 Extensions: ase-3.22.1, Pint-0.22, pydantic-1.9.1, qcelemental-0.27.1, xtb-6.6.1 Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 5,549: / Line 4,779: @@
 | align="center" | 0.24.2, 0.25.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: xtensor is a C++ library meant for numerical analysis with multi-dimensional array expressions. Homepage: https://github.com/xtensor-stack/xtensor URL: https://github.com/xtensor-stack/xtensor<br /><br /><br /></div>
-|-
-| align="center" | [http://yaehmop.sourceforge.net/ yaehmop]
-| align="center" | chem
-| align="center" | 3.0.3
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: "Yet Another extended Huckel Molecular Orbital Package (YAeHMOP) was developed by Greg Landrum whilest a graduate student in the research group of Professor Roald Hoffmann at Cornell University. YAeHMOP is intended to be an easy to use, transparent, extended Huckel calculation and visualization package which can perform calculations on both molecular and extended materials in 1,2, or 3 dimensions. Homepage: http://yaehmop.sourceforge.net/ Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [http://www.yambo-code.org yambo]
@@ Line 5,567: / Line 4,792: @@
 | align="center" | [https://www.dkrz.de/redmine/projects/yaxt yaxt]
 | align="center" | tools
-| align="center" | 0.5.1, 0.6.0, 0.9.0, 0.9.1, 0.10.0
+| align="center" | 0.9.0, 0.9.1, 0.10.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Yet Another eXchange Tool Homepage: https://www.dkrz.de/redmine/projects/yaxt URL: https://www.dkrz.de/redmine/projects/yaxt Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 5,574: / Line 4,799: @@
 | align="center" | 0.3
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Zeo++ is a software package for analysis of crystalline porous materials. Zeo++ can be used to perform geometry-based analysis of structure and topology of the void space inside a material, to assemble or alternate structures as well as to generate structure representations to be used in structure similarity calculations. Zeo++ can be used to either analyze a single structure or perform high-throughput analysis of a large database. Homepage: https://www.zeoplusplus.org/ URL: https://www.zeoplusplus.org/<br /><br /><br /></div>
-|-
-| align="center" | [http://www.zeromq.org/ zeromq]
-| align="center" | tools
-| align="center" | 4.2.5
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems. Homepage: http://www.zeromq.org/ Keyword:tools<br /><br /><br /></div>
 |}<noinclude>{{NOINDEX}}</noinclude>

Modules avx512: Difference between revisions

Modules avx512 (view source)

Revision as of 20:19, 8 July 2024