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! style="width: 15%" align="center" | Documentation
! style="width: 15%" align="center" | Documentation
! align="center" | Description
! align="center" | Description
|-
| align="center" | [http://www.simulia.com/products/abaqus_fea.html abaqus/6.14.1]
| align="center" | phys
| align="center" |
| <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 Keyword:phys<br />'''Prerequisites:''' -<br />'''Description:''' </div>
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| align="center" | [http://www.abinit.org/ abinit/8.2.2]
| align="center" | chem
| align="center" | [[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/ Keyword:chem CC-Wiki: ABINIT<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.bcgsc.ca/platform/bioinfo/software/abyss abyss/1.5.2]
| align="center" | bio
| align="center" |
| <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: http://www.bcgsc.ca/platform/bioinfo/software/abyss Keyword:bio<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.bcgsc.ca/platform/bioinfo/software/abyss abyss/1.9.0]
| align="center" | bio
| align="center" |
| <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: http://www.bcgsc.ca/platform/bioinfo/software/abyss Keyword:bio<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [https://www.genetics.ucla.edu/software/admixture admixture/1.3.0]
| align="center" | bio
| align="center" |
| <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://www.genetics.ucla.edu/software/admixture Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://software.intel.com/intel-advisor-xe advisor/2018.3]
| align="center" | tools
| align="center" |
| <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 Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://afni.nimh.nih.gov/ afni/20180404]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://www.popgen.dk/angsd angsd/0.918]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Program for analysing NGS data. Homepage: http://www.popgen.dk/angsd Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://annovar.openbioinformatics.org/en/latest/ annovar/2017Jul16]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' - or gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.ansys.com ansys/17.2]
| align="center" | phys
| align="center" | [[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 Keyword:phys CC-Wiki: ANSYS<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.ansys.com ansys/18.1]
| align="center" | phys
| align="center" | [[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 Keyword:phys CC-Wiki: ANSYS<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.ansys.com ansys/18.2]
| align="center" | phys
| align="center" | [[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 Keyword:phys CC-Wiki: ANSYS<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.ansys.com ansys/19.1]
| align="center" | phys
| align="center" | [[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 Keyword:phys CC-Wiki: ANSYS<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/appleseedhq/appleseed appleseed/1.8.1-beta]
| align="center" | vis
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: appleseed is an open source, physically-based global illumination rendering engine primarily designed for animation and visual effects. Homepage: https://github.com/appleseedhq/appleseed Keyword:vis<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
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| align="center" | [http://arma.sourceforge.net/ armadillo/7.950.1]
| align="center" | math
| align="center" |
| <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: http://arma.sourceforge.net/ Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://forge.scilab.org/index.php/p/arpack-ng/ arpack-ng/3.4.0]
| align="center" | math
| align="center" |
| <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: http://forge.scilab.org/index.php/p/arpack-ng/ Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://forge.scilab.org/index.php/p/arpack-ng/ arpack-ng/3.5.0]
| align="center" | math
| align="center" |
| <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: http://forge.scilab.org/index.php/p/arpack-ng/ Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://downloads.asperasoft.com/ ascp/3.5.4]
| align="center" | tools
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/pezmaster31/bamtools bamtools/2.4.1]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://genome.sph.umich.edu/wiki/BamUtil bamutil/1.0.13]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
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| align="center" | [http://bazel.io/ bazel/0.11.1]
| align="center" | tools
| align="center" |
| <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: http://bazel.io/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://bazel.io/ bazel/0.19.2]
| align="center" | tools
| align="center" |
| <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: http://bazel.io/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://bazel.io/ bazel/0.5.2]
| align="center" | tools
| align="center" |
| <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: http://bazel.io/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://bazel.io/ bazel/0.7.0]
| align="center" | tools
| align="center" |
| <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: http://bazel.io/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
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| align="center" | [https://sourceforge.net/projects/bbmap/ bbmap/37.36]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
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| align="center" | [http://www.htslib.org/ bcftools/1.4]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants - Homepage: http://www.htslib.org/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.htslib.org/ bcftools/1.5]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants Homepage: http://www.htslib.org/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/beagle-dev/beagle-lib beagle-lib/2.1.2]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://beast2.org/ beast/2.4.0]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/arq5x/bedtools2 bedtools/2.26.0]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.bioperl.org/ bioperl/1.7.1]
| align="center" | bio
| align="center" |
| <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: http://www.bioperl.org/ Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
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| align="center" | [http://blast.ncbi.nlm.nih.gov/ blast+/2.6.0]
| align="center" | bio
| align="center" |
| <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: http://blast.ncbi.nlm.nih.gov/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
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| align="center" | [http://genome.ucsc.edu/FAQ/FAQblat.html blat/3.5]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. - Homepage: http://genome.ucsc.edu/FAQ/FAQblat.html Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [https://data.broadinstitute.org/alkesgroup/BOLT-LMM/ bolt-lmm/2.2]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
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| align="center" | [http://www.boost.org/ boost-mpi/1.60.0]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: http://www.boost.org/ Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.boost.org/ boost-mpi/1.65.1]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: http://www.boost.org/ Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0 and cuda/8.0.44 and openmpi/2.1.1 or gcc/5.4.0 and cuda/9.0.176 and openmpi/2.1.1 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and cuda/9.0.176 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.boost.org/ boost/1.60.0]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: http://www.boost.org/ Keyword:tools<br />'''Prerequisites:''' gcc/4.8.5 or gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.boost.org/ boost/1.63.0]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: http://www.boost.org/ Keyword:tools<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.boost.org/ boost/1.65.1]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: http://www.boost.org/ Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0 or gcc/6.4.0 or intel/2016.4 or intel/2017.1 or intel/2017.5<br />'''Description:''' </div>
|-
| align="center" | [http://bowtie-bio.sourceforge.net/index.shtml bowtie/1.1.2]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml bowtie2/2.3.0]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://bio-bwa.sourceforge.net/ bwa/0.7.15]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/caffe2/caffe2 caffe2/0.8.1]
| align="center" | ai
| align="center" | [[Caffe2]]
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Caffe2 is a lightweight, modular, and scalable deep learning framework. Building on the original Caffe, Caffe2 is designed with expression, speed, and modularity in mind. Homepage: https://github.com/caffe2/caffe2 Keyword:ai CC-Wiki: Caffe2<br />'''Prerequisites:''' gcc/5.4.0 and cuda/8.0.44<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/marbl/canu canu/1.5]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/marbl/canu canu/1.6]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/Illumina/canvas canvas/1.25]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://seq.cs.iastate.edu/ cap3/20151002]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.cesm.ucar.edu/models/ccsm4.0/ ccsm/4_0_a02]
| align="center" | geo
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://code.zmaw.de/projects/cdo cdo/1.7.2]
| align="center" | geo
| align="center" |
| <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 Keyword:geo<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome cellranger/2.1.0]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/infphilo/centrifuge centrifuge/1.0.3-beta]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.cesm.ucar.edu/models/cesm1.2/ cesm/1_2_2]
| align="center" | geo
| align="center" |
| <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/cesm1.2/ Keyword:geo<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.cgal.org/ cgal/4.9]
| align="center" | math
| align="center" |
| <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: http://www.cgal.org/ Keyword:math<br />'''Prerequisites:''' gcc/4.8.5 or gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [https://cgns.github.io/ cgns/3.3.1]
| align="center" | phys
| align="center" |
| <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/ Keyword:phys<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://chapel.cray.com chapel-single/1.15.0]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Chapel is an emerging parallel programming language whose design and development is being led by Cray Inc. Chapel is designed to improve the productivity of high-end computer users while also serving as a portable parallel programming model that can be used on commodity clusters or desktop multicore systems. Chapel strives to vastly improve the programmability of large-scale parallel computers while matching or beating the performance and portability of current programming models like MPI. Homepage: http://chapel.cray.com Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://chapel.cray.com chapel-slurm-gasnetrun_ibv/1.15.0]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Chapel is an emerging parallel programming language whose design and development is being led by Cray Inc. Chapel is designed to improve the productivity of high-end computer users while also serving as a portable parallel programming model that can be used on commodity clusters or desktop multicore systems. Chapel strives to vastly improve the programmability of large-scale parallel computers while matching or beating the performance and portability of current programming models like MPI. Homepage: http://chapel.cray.com Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://circos.ca/documentation/ circos/0.69-6]
| align="center" | vis
| align="center" |
| <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. There are other reasons why a circular layout is advantageous, not the least being the fact that it is attractive. Circos is ideal for creating publication-quality infographics and illustrations with a high data-to-ink ratio, richly layered data and pleasant symmetries. You have fine control each element in the figure to tailor its focus points and detail to your audience. Homepage: http://circos.ca/documentation/ Keyword:vis<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://clang.llvm.org/ clang/3.8.1]
| align="center" | tools
| align="center" |
| <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: http://clang.llvm.org/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://clang.llvm.org/ clang/3.9.0]
| align="center" | tools
| align="center" |
| <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: http://clang.llvm.org/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://proj-clhep.web.cern.ch/proj-clhep/ clhep/2.3.1.1]
| align="center" | math
| align="center" |
| <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: http://proj-clhep.web.cern.ch/proj-clhep/ Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.cmake.org cmake/3.12.3]
| align="center" | tools
| align="center" |
| <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: http://www.cmake.org Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/abyzovlab/CNVnator cnvnator/0.3.3]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads Homepage: https://github.com/abyzovlab/CNVnator Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [https://www.comsol.com comsol/5.3a]
| align="center" | phys
| align="center" |
| <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 Keyword:phys<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://www.comsol.com comsol/5.4]
| align="center" | phys
| align="center" |
| <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 Keyword:phys<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.cp2k.org/ cp2k/4.1]
| align="center" | chem
| align="center" |
| <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: http://www.cp2k.org/ Keyword:chem<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.cp2k.org/ cp2k/6.1]
| align="center" | chem
| align="center" |
| <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: http://www.cp2k.org/ Keyword:chem<br />'''Prerequisites:''' intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://cpmd.org cpmd/3.17.1]
| align="center" | chem
| align="center" |
| <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 Keyword:chem<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://cromwell.readthedocs.io/ cromwell/34]
| align="center" | tools
| align="center" |
| <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/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://www.cst.com/ cst/2017]
| align="center" | phys
| align="center" |
| <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/ Keyword:phys<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://www.cst.com/ cst/2018]
| align="center" | phys
| align="center" |
| <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/ Keyword:phys<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://developer.nvidia.com/cuda-toolkit cuda/10.0.130]
| align="center" | tools
| align="center" | [[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 Keyword:tools CC-Wiki: CUDA<br />'''Prerequisites:''' gcc/7.3.0<br />'''Description:''' </div>
|-
| align="center" | [https://developer.nvidia.com/cuda-toolkit cuda/7.5.18]
| align="center" | tools
| align="center" | [[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 Keyword:tools CC-Wiki: CUDA<br />'''Prerequisites:''' gcc/4.8.5<br />'''Description:''' </div>
|-
| align="center" | [https://developer.nvidia.com/cuda-toolkit cuda/8.0.44]
| align="center" | tools
| align="center" | [[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 Keyword:tools CC-Wiki: CUDA<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or pgi/17.3<br />'''Description:''' </div>
|-
| align="center" | [https://developer.nvidia.com/cuda-toolkit cuda/9.0.176]
| align="center" | tools
| align="center" | [[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 Keyword:tools CC-Wiki: CUDA<br />'''Prerequisites:''' gcc/5.4.0 or gcc/6.4.0 or intel/2016.4 or pgi/17.3<br />'''Description:''' </div>
|-
| align="center" | [https://developer.nvidia.com/cudnn cudnn/5.1]
| align="center" | math
| align="center" |
| <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 Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 and cuda/8.0.44 or intel/2016.4 and cuda/8.0.44<br />'''Description:''' </div>
|-
| align="center" | [https://developer.nvidia.com/cudnn cudnn/6.0]
| align="center" | math
| align="center" |
| <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 Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 and cuda/8.0.44 or intel/2016.4 and cuda/8.0.44<br />'''Description:''' </div>
|-
| align="center" | [https://developer.nvidia.com/cudnn cudnn/7.0]
| align="center" | math
| align="center" |
| <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 Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 and cuda/8.0.44 or gcc/5.4.0 and cuda/9.0.176 or intel/2016.4 and cuda/8.0.44 or intel/2016.4 and cuda/9.0.176<br />'''Description:''' </div>
|-
| align="center" | [https://developer.nvidia.com/cudnn cudnn/7.4]
| align="center" | math
| align="center" |
| <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 Keyword:math<br />'''Prerequisites:''' gcc/7.3.0 and cuda/10.0.130<br />'''Description:''' </div>
|-
| align="center" | [http://cole-trapnell-lab.github.io/cufflinks/ cufflinks/2.2.1]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [https://sourceforge.net/projects/cunit/ cunit/2.1-3]
| align="center" | tools
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.allinea.com ddt-cpu/18.3]
| align="center" | tools
| align="center" | [[ARM software]]
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Profiler and debugger, combining Arm MAP and Arm DDT. Homepage: http://www.allinea.com CC-Wiki: ARM software<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.allinea.com ddt-cpu/7.1]
| align="center" | tools
| align="center" | [[ARM software]]
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Profiler and debugger, combining Allinea MAP and Allinea DDT. Homepage: http://www.allinea.com CC-Wiki: ARM software<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.allinea.com ddt-gpu/18.3]
| align="center" | tools
| align="center" | [[ARM software]]
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Profiler and debugger, combining Arm MAP and Arm DDT, with support for CUDA. Homepage: http://www.allinea.com CC-Wiki: ARM software<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.allinea.com ddt-gpu/7.1]
| align="center" | tools
| align="center" | [[ARM software]]
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Profiler and debugger, combining Allinea MAP and Allinea DDT, with support for CUDA. Homepage: http://www.allinea.com CC-Wiki: ARM software<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.dealii.org/ dealii/8.5.0]
| align="center" | math
| align="center" |
| <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 />'''Prerequisites:''' intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/dellytools/delly delly/0.7.8]
| align="center" | -
| align="center" |
| <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. Homepage: https://github.com/dellytools/delly<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/bbuchfink/diamond diamond/0.9.8]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://www.scd.stfc.ac.uk/SCD/44516.aspx dl_poly4/4.08]
| align="center" | chem
| align="center" |
| <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 Keyword:chem<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [https://www.microsoft.com/net/ dotnet-core-runtime/1.1.8]
| align="center" | tools
| align="center" |
| <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. Homepage: https://www.microsoft.com/net/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://www.microsoft.com/net/ dotnet-core-runtime/2.0.7]
| align="center" | tools
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://www.perl.org/ eclipse/4.6.0]
| align="center" | tools
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://eigen.tuxfamily.org/index.php?title=Main_Page eigen/3.2.10]
| align="center" | math
| align="center" |
| <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: http://eigen.tuxfamily.org/index.php?title=Main_Page Keyword:math<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://eigen.tuxfamily.org/index.php?title=Main_Page eigen/3.2.2]
| align="center" | math
| align="center" |
| <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: http://eigen.tuxfamily.org/index.php?title=Main_Page Keyword:math<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://eigen.tuxfamily.org/index.php?title=Main_Page eigen/3.3.2]
| align="center" | math
| align="center" |
| <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: http://eigen.tuxfamily.org/index.php?title=Main_Page Keyword:math<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://eigen.tuxfamily.org/index.php?title=Main_Page eigen/3.3.5]
| align="center" | math
| align="center" |
| <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: http://eigen.tuxfamily.org/index.php?title=Main_Page Keyword:math<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://elpa.rzg.mpg.de elpa/2017.11.001]
| align="center" | math
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Eigenvalue SoLvers for Petaflop-Applications . Homepage: http://elpa.rzg.mpg.de Keyword:math<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.erlang.org/ erlangotp/20.0]
| align="center" | tools
| align="center" |
| <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/ Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://sourceforge.net/projects/esmf esmf/7.0.1]
| align="center" | geo
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models. Homepage: http://sourceforge.net/projects/esmf Keyword:geo<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [https://bitbucket.org/jerlar73/fast-gbs fast-gbs/2017-01-25]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ fastqc/0.11.5]
| align="center" | bio
| align="center" |
| <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: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ fastqc/0.11.8]
| align="center" | bio
| align="center" |
| <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: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://cmpg.unibe.ch/software/fastsimcoal2/ fastsimcoal2/2.6.0.3]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: While preserving all the simulation flexibility of simcoal2, fastsimcoal is now implemented under a faster continous-time sequential Markovian coalescent approximation, allowing it to efficiently generate genetic diversity for different types of markers along large genomic regions, for both present or ancient samples. It includes a parameter sampler allowing its integration into Bayesian or likelihood parameter estimation procedure. fastsimcoal can handle very complex evolutionary scenarios including an arbitrary migration matrix between samples, historical events allowing for population resize, population fusion and fission, admixture events, changes in migration matrix, or changes in population growth rates. The time of sampling can be specified independently for each sample, allowing for serial sampling in the same or in different populations. Homepage: http://cmpg.unibe.ch/software/fastsimcoal2/ Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.microbesonline.org/fasttree/ fasttree/2.1.10]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://hannonlab.cshl.edu/fastx_toolkit/ fastx-toolkit/0.0.14]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Homepage: http://hannonlab.cshl.edu/fastx_toolkit/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [https://altairhyperworks.com/product/FEKO feko/2018]
| align="center" | phys
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.fftw.org fftw-mpi/2.1.5]
| align="center" | math
| align="center" |
| <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: http://www.fftw.org Keyword:math<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.fftw.org fftw-mpi/3.3.6]
| align="center" | math
| align="center" |
| <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: http://www.fftw.org Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/1.8.8 or gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or gcc/6.4.0 and cuda/9.0.176 and openmpi/2.1.1 or gcc/6.4.0 and openmpi/2.1.1 or intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.fftw.org fftw/3.3.6]
| align="center" | math
| align="center" |
| <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: http://www.fftw.org Keyword:math<br />'''Prerequisites:''' gcc/4.8.5 or gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/rrwick/Filtlong filtlong/0.2.0]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://www.ansys.com/products/fluids/ansys-fluent fluent/16.1]
| align="center" | phys
| align="center" | [[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 CC-Wiki: ANSYS<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://sourceforge.net/projects/freepascal/ fpc/3.0.0]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A 32/64/16-bit Pascal compiler for Win32/64/CE, Linux, Mac OS X/iOS, FreeBSD, OS/2, Game Boy Advance, Nintendo NDS and DOS; semantically compatible with Delphi, Borland Pascal and Mac Pascal (partially) with extra features, e.g. operator overloading. Homepage: https://sourceforge.net/projects/freepascal/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/ekg/freebayes freebayes/1.1.0]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bayesian haplotype-based polymorphism discovery and genotyping. Homepage: https://github.com/ekg/freebayes Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki freesurfer/5.3.0]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data. Homepage: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/ctSkennerton/fxtract fxtract/2.3]
| align="center" | -
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ g2clib/1.6.0]
| align="center" | geo
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Library contains GRIB2 encoder/decoder ('C' version). Homepage: http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ Keyword:geo<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ g2lib/1.4.0]
| align="center" | geo
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Library contains GRIB2 encoder/decoder and search/indexing routines. Homepage: http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ Keyword:geo<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.msg.chem.iastate.edu/gamess/index.html gamess-us/20170420-R1]
| align="center" | chem
| align="center" |
| <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. Homepage: http://www.msg.chem.iastate.edu/gamess/index.html Keyword:chem<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.broadinstitute.org/gatk/ gatk-queue/3.8-0]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.broadinstitute.org/gatk/ gatk/3.7]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.broadinstitute.org/gatk/ gatk/3.8]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.broadinstitute.org/gatk/ gatk/4.0.0.0]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.broadinstitute.org/gatk/ gatk/4.0.12.0]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.broadinstitute.org/gatk/ gatk/4.0.8.1]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.broadinstitute.org/gatk/ gatk/4.1.0.0]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://gcc.gnu.org/ gcc/4.8.5]
| align="center" | tools
| align="center" |
| <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: http://gcc.gnu.org/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://gcc.gnu.org/ gcc/4.9.4]
| align="center" | tools
| align="center" |
| <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: http://gcc.gnu.org/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://gcc.gnu.org/ gcc/5.4.0]
| align="center" | tools
| align="center" |
| <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: http://gcc.gnu.org/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://gcc.gnu.org/ gcc/6.4.0]
| align="center" | tools
| align="center" |
| <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: http://gcc.gnu.org/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://gcc.gnu.org/ gcc/7.3.0]
| align="center" | tools
| align="center" |
| <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: http://gcc.gnu.org/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.gdal.org/ gdal/2.1.3]
| align="center" | geo
| align="center" |
| <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: http://www.gdal.org/ Keyword:geo<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.gdal.org/ gdal/2.2.1]
| align="center" | geo
| align="center" |
| <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: http://www.gdal.org/ Keyword:geo<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://geant4.cern.ch/ geant4/10.02.p03]
| align="center" | phys
| align="center" |
| <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: http://geant4.cern.ch/ Keyword:phys<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://trac.osgeo.org/geos geos/3.6.1]
| align="center" | geo
| align="center" |
| <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: http://trac.osgeo.org/geos Keyword:geo<br />'''Prerequisites:''' gcc/5.4.0 or gcc/6.4.0 or intel/2016.4 or intel/2017.1 or intel/2017.5<br />'''Description:''' </div>
|-
| align="center" | [http://git-annex.branchable.com/ git-annex/6.20180807]
| align="center" | tools
| align="center" |
| <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/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/g-truc/glm glm/0.9.7.2]
| align="center" | vis
| align="center" |
| <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 Keyword:vis<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://www.gnu.org/software/glpk/ glpk/4.61]
| align="center" | math
| align="center" |
| <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/ Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://research-pub.gene.com/gmap/ gmap-gsnap/2017-04-13]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.golang.org go/1.10.3]
| align="center" | tools
| align="center" |
| <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: http://www.golang.org Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://grackle.readthedocs.io grackle/2.1]
| align="center" | phys
| align="center" |
| <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 />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.gromacs.org gromacs-plumed/2016.3]
| align="center" | chem
| align="center" | [[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 Keyword:chem CC-Wiki: GROMACS<br />'''Prerequisites:''' intel/2016.4 and cuda/8.0.44 and openmpi/2.0.2 or intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.gromacs.org gromacs/2016.3]
| align="center" | chem
| align="center" | [[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. simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS - Homepage: http://www.gromacs.org Keyword:chem CC-Wiki: GROMACS<br />'''Prerequisites:''' intel/2016.4 and cuda/8.0.44 and openmpi/2.0.2 or intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.gromacs.org gromacs/2018]
| align="center" | chem
| align="center" | [[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. simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org Keyword:chem CC-Wiki: GROMACS<br />'''Prerequisites:''' gcc/6.4.0 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.gromacs.org gromacs/2018.1]
| align="center" | chem
| align="center" | [[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. simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org Keyword:chem CC-Wiki: GROMACS<br />'''Prerequisites:''' gcc/6.4.0 and cuda/9.0.176 and openmpi/2.1.1 or gcc/6.4.0 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.gromacs.org gromacs/4.6.7]
| align="center" | chem
| align="center" | [[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. simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS - Homepage: http://www.gromacs.org Keyword:chem CC-Wiki: GROMACS<br />'''Prerequisites:''' intel/2016.4 and cuda/8.0.44 and openmpi/2.0.2 or intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.gromacs.org gromacs/5.0.7]
| align="center" | chem
| align="center" | [[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. - Homepage: http://www.gromacs.org Keyword:chem CC-Wiki: GROMACS<br />'''Prerequisites:''' intel/2016.4 and cuda/8.0.44 and openmpi/2.0.2 or intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.gromacs.org gromacs/5.1.4]
| align="center" | chem
| align="center" | [[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. - Homepage: http://www.gromacs.org Keyword:chem CC-Wiki: GROMACS<br />'''Prerequisites:''' intel/2016.4 and cuda/8.0.44 and openmpi/2.0.2 or intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.gnu.org/software/gsl/ gsl/1.16]
| align="center" | math
| align="center" |
| <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: http://www.gnu.org/software/gsl/ Keyword:math<br />'''Prerequisites:''' gcc/4.8.5 or gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.gnu.org/software/gsl/ gsl/2.2.1]
| align="center" | math
| align="center" |
| <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: http://www.gnu.org/software/gsl/ Keyword:math<br />'''Prerequisites:''' gcc/4.8.5 or gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.gnu.org/software/gsl/ gsl/2.3]
| align="center" | math
| align="center" |
| <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: http://www.gnu.org/software/gsl/ Keyword:math<br />'''Prerequisites:''' gcc/4.8.5 or gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [https://www.gtk.org/ gtk+3/3.20.9]
| align="center" | tools
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.gnu.org/software/guile guile/1.8.8]
| align="center" | tools
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.hdfgroup.org/h4toh5/ h4toh5/2.2.2]
| align="center" | io
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects. Homepage: http://www.hdfgroup.org/h4toh5/ Keyword:io<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.hdfgroup.org/products/hdf4/ hdf/4.2.12]
| align="center" | io
| align="center" |
| <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: http://www.hdfgroup.org/products/hdf4/ Keyword:io<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.hdfgroup.org/HDF5/ hdf5-mpi/1.8.18]
| align="center" | io
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. Homepage: http://www.hdfgroup.org/HDF5/ Keyword:io<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or gcc/6.4.0 and openmpi/2.1.1 or intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.hdfgroup.org/HDF5/ hdf5/1.8.18]
| align="center" | io
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. Homepage: http://www.hdfgroup.org/HDF5/ Keyword:io<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [https://ccb.jhu.edu/software/hisat2/index.shtml hisat2/2.1.0]
| align="center" | bio
| align="center" |
| <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://ccb.jhu.edu/software/hisat2/index.shtml Keyword:bio<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://hmmer.org/ hmmer/2.3.2]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://hmmer.org/ hmmer/3.1b2]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.netlib.org/benchmark/hpl/ hpl/2.2]
| align="center" | tools
| align="center" |
| <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: http://www.netlib.org/benchmark/hpl/ Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1 or pgi/17.3 and openmpi/2.0.2 or pgi/17.3 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.htslib.org/ htslib/1.4]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix - Homepage: http://www.htslib.org/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.htslib.org/ htslib/1.5]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix Homepage: http://www.htslib.org/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://www.ncbi.nlm.nih.gov/igblast/intro.html igblast/1.7.0]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://igraph.org igraph/0.7.1]
| align="center" | math
| align="center" |
| <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: http://igraph.org Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://software.intel.com/en-us/intel-mkl/ imkl/11.1.4.214]
| align="center" | math
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. Homepage: http://software.intel.com/en-us/intel-mkl/ Keyword:math<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://software.intel.com/en-us/intel-mkl/ imkl/11.3.4.258]
| align="center" | math
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. Homepage: http://software.intel.com/en-us/intel-mkl/ Keyword:math<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://software.intel.com/en-us/intel-mkl/ imkl/2017.1.132]
| align="center" | math
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. Homepage: http://software.intel.com/en-us/intel-mkl/ Keyword:math<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://software.intel.com/en-us/intel-mkl/ imkl/2017.4.239]
| align="center" | math
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. Homepage: http://software.intel.com/en-us/intel-mkl/ Keyword:math<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://software.intel.com/en-us/intel-mkl/ imkl/2018.1.163]
| align="center" | math
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. Homepage: http://software.intel.com/en-us/intel-mkl/ Keyword:math<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://software.intel.com/en-us/intel-mkl/ imkl/2018.3.222]
| align="center" | math
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. Homepage: http://software.intel.com/en-us/intel-mkl/ Keyword:math<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://software.intel.com/en-us/intel-mkl/ imkl/2019.2.187]
| align="center" | math
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. Homepage: http://software.intel.com/en-us/intel-mkl/ Keyword:math<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://mathgen.stats.ox.ac.uk/impute/impute_v2.html impute2/2.3.2]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://software.intel.com/en-us/intel-inspector-xe inspector/2018.3]
| align="center" | tools
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ intel/2014.6]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel C, C++ and Fortran compilers Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ intel/2016.4]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ intel/2017.1]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ intel/2017.5]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel C, C++ and Fortran compilers Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ intel/2018.3]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel C, C++ and Fortran compilers Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.ebi.ac.uk/interpro/ interproscan/5.23-62.0]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://software.intel.com/en-us/articles/intel-ipp/ ipp/2017.1.132]
| align="center" | tools
| align="center" |
| <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: http://software.intel.com/en-us/articles/intel-ipp/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://software.intel.com/en-us/articles/intel-ipp/ ipp/9.0.4]
| align="center" | tools
| align="center" |
| <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: http://software.intel.com/en-us/articles/intel-ipp/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.iqtree.org/ iq-tree/1.5.5]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Efficient phylogenomic software by maximum likelihood Homepage: http://www.iqtree.org/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://software.intel.com/en-us/intel-trace-analyzer/ itac/2018.3.022]
| align="center" | tools
| align="center" |
| <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: http://software.intel.com/en-us/intel-trace-analyzer/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://itk.org itk/4.12.2]
| align="center" | vis
| align="center" |
| <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 Keyword:vis<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://mcmc-jags.sourceforge.net/ jags/4.2.0]
| align="center" | math
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation - Homepage: http://mcmc-jags.sourceforge.net/ Keyword:math<br />'''Prerequisites:''' intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.ece.uvic.ca/~frodo/jasper/ jasper/1.900.1]
| align="center" | vis
| align="center" |
| <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: http://www.ece.uvic.ca/~frodo/jasper/ Keyword:vis<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://java.com/ java/1.7.0_80]
| align="center" | tools
| align="center" | [[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://java.com/ Keyword:tools CC-Wiki: Java<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://java.com/ java/1.8.0_121]
| align="center" | tools
| align="center" | [[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://java.com/ Keyword:tools CC-Wiki: Java<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://java.com/ java/1.8.0_192]
| align="center" | tools
| align="center" | [[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://java.com/ Keyword:tools CC-Wiki: Java<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.cbcb.umd.edu/software/jellyfish/ jellyfish/1.1.11]
| align="center" | bio
| align="center" |
| <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.cbcb.umd.edu/software/jellyfish/ Keyword:bio<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.genome.umd.edu/jellyfish.html jellyfish/2.2.6]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://julialang.org julia/0.5.1]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A high-level, high-performance dynamic language for technical computing. Homepage: http://julialang.org Keyword:tools<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://julialang.org julia/0.6.0]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A high-level, high-performance dynamic language for technical computing. Homepage: http://julialang.org Keyword:tools<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://julialang.org julia/1.0.0]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A high-level, high-performance dynamic language for technical computing. Homepage: http://julialang.org Keyword:tools<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://julialang.org julia/1.0.2]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A high-level, high-performance dynamic language for technical computing. Homepage: http://julialang.org Keyword:tools<br />'''Prerequisites:''' gcc/7.3.0<br />'''Description:''' </div>
|-
| align="center" | [http://pachterlab.github.io/kallisto/ kallisto/0.44.0]
| align="center" | bio
| align="center" |
| <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: http://pachterlab.github.io/kallisto/ Keyword:bio<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://openkim.org/ kim/1.8.2]
| align="center" | chem
| align="center" |
| <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/ Keyword:chem<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://ccb.jhu.edu/software/kraken/ kraken/0.10.5-beta]
| align="center" | bio
| align="center" |
| <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: http://ccb.jhu.edu/software/kraken/ Keyword:bio<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://lammps.sandia.gov/ lammps-omp/20170331]
| align="center" | chem
| align="center" |
| <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: -MSCG, -GPU, -KOKKOS, -KIM, -USER-QUIP, -USER-INTEL, -USER-VTK Homepage: http://lammps.sandia.gov/ Keyword:chem<br />'''Prerequisites:''' intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://lammps.sandia.gov/ lammps-omp/20170811]
| align="center" | chem
| align="center" |
| <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, -MSCG, -USER-INTEL, -USER-QUIP Homepage: http://lammps.sandia.gov/ Keyword:chem<br />'''Prerequisites:''' intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://lammps.sandia.gov/ lammps-user-intel/20170331]
| align="center" | chem
| align="center" |
| <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: -MSCG, -GPU, -KOKKOS, -KIM, -USER-QUIP, -USER-VTK, -QEQ, -USER-ATC, -MANYBODY Homepage: http://lammps.sandia.gov/ Keyword:chem<br />'''Prerequisites:''' intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://lammps.sandia.gov/ lammps-user-intel/20170811]
| align="center" | chem
| align="center" |
| <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 />'''Prerequisites:''' intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://lammps.sandia.gov/ lammps/20170331]
| align="center" | chem
| align="center" |
| <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: -MSCG, -GPU, -KOKKOS, -KIM, -USER-QUIP, -USER-OMP, -OPT, -USER-MISC, -USER-INTEL, -USER-VTK Homepage: http://lammps.sandia.gov/ Keyword:chem<br />'''Prerequisites:''' intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.hyperrealm.com/libconfig/ libconfig/1.7.2]
| align="center" | tools
| align="center" |
| <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 />'''Prerequisites:''' gcc/7.3.0<br />'''Description:''' </div>
|-
| align="center" | [http://deeplearning.net/software/libgpuarray libgpuarray/0.6.9]
| align="center" | math
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Homepage: http://deeplearning.net/software/libgpuarray Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 and cuda/8.0.44 or intel/2016.4 and cuda/8.0.44<br />'''Description:''' </div>
|-
| align="center" | [http://hannonlab.cshl.edu/fastx_toolkit/ libgtextutils/0.7]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://sourceforge.net/p/libint/ libint/1.1.6]
| align="center" | chem
| align="center" |
| <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://sourceforge.net/p/libint/ Keyword:chem<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/evaleev/libint libint/2.2.0]
| align="center" | chem
| align="center" |
| <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 Keyword:chem<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/libMesh/libmesh libmesh/1.2.1]
| align="center" | math
| align="center" |
| <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 Keyword:math<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.tddft.org/programs/octopus/wiki/index.php/Libxc libxc/3.0.0]
| align="center" | chem
| align="center" |
| <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: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc Keyword:chem<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.tddft.org/programs/octopus/wiki/index.php/Libxc libxc/4.2.1]
| align="center" | chem
| align="center" |
| <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: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc Keyword:chem<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/hfp/libxsmm libxsmm/1.8]
| align="center" | math
| align="center" |
| <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 Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://llvm.org/ llvm/6.0.1]
| align="center" | tools
| align="center" |
| <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: http://llvm.org/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.lstc.com/products/ls-opt ls-opt/5.2.1]
| align="center" | phys
| align="center" |
| <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 Keyword:phys<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/arq5x/lumpy-sv lumpy/0.2.13]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://csg.sph.umich.edu/abecasis/MACH/ mach/1.0.18]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://mafft.cbrc.jp/alignment/software/ mafft/7.310]
| align="center" | bio
| align="center" |
| <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; ~10,000 sequences), etc. Homepage: http://mafft.cbrc.jp/alignment/software/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://icl.cs.utk.edu/magma/ magma/2.2.0]
| align="center" | math
| align="center" |
| <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: http://icl.cs.utk.edu/magma/ Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 and cuda/8.0.44 or intel/2016.4 and cuda/8.0.44<br />'''Description:''' </div>
|-
| align="center" | [http://icl.cs.utk.edu/magma/ magma/2.4.0]
| align="center" | math
| align="center" |
| <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: http://icl.cs.utk.edu/magma/ Keyword:math<br />'''Prerequisites:''' gcc/7.3.0 and cuda/10.0.130<br />'''Description:''' </div>
|-
| align="center" | [http://www.gnu.org/software/make/make.html make/3.82]
| align="center" | tools
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/Illumina/manta manta/1.2.2]
| align="center" | bio
| align="center" |
| <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. The method is designed for rapid analysis on standard compute hardware: NA12878 at 50x genomic coverage is analyzed in less than 20 minutes on a 20 core server, and most WGS tumor/normal analyses can be completed within 2 hours. Manta combines paired and split-read evidence during SV discovery and scoring to improve accuracy, but does not require split-reads or successful breakpoint assemblies to report a variant in cases where there is strong evidence otherwise. It provides scoring models for germline variants in small sets of diploid samples and somatic variants in matched tumor/normal sample pairs. There is experimental support for analysis of unmatched tumor samples as well. Manta accepts input read mappings from BAM or CRAM files and reports all SV and indel inferences in VCF 4.1 format. See the user guide for a full description of capabilities and limitations. Homepage: https://github.com/Illumina/manta Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://mariadb.org/ mariadb/10.1.21]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MariaDB An enhanced, drop-in replacement for MySQL. Homepage: https://mariadb.org/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://sourceforge.net/projects/matio/ matio/1.5.2]
| align="center" | io
| align="center" |
| <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: http://sourceforge.net/projects/matio/ Keyword:io<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.mathworks.com/products/matlab matlab/2014a]
| align="center" | tools
| align="center" | [[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 Keyword:tools CC-Wiki: MATLAB<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.mathworks.com/products/matlab matlab/2016b]
| align="center" | tools
| align="center" | [[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 Keyword:tools CC-Wiki: MATLAB<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.mathworks.com/products/matlab matlab/2017a]
| align="center" | tools
| align="center" | [[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 Keyword:tools CC-Wiki: MATLAB<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.mathworks.com/products/matlab matlab/2018a]
| align="center" | tools
| align="center" | [[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 Keyword:tools CC-Wiki: MATLAB<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.mathworks.com/products/matlab matlab/2018b]
| align="center" | tools
| align="center" | [[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 Keyword:tools CC-Wiki: MATLAB<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://maven.apache.org/index.html maven/3.5.0]
| align="center" | tools
| align="center" |
| <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: http://maven.apache.org/index.html Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html maxbin/2.2.4]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users can understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic sequences and the reads coverage information or sequencing reads. For users convenience MaxBin will report genome-related statistics, including estimated completeness, GC content and genome size in the binning summary page. Users can use MEGAN or similar software on MaxBin bins to find the taxonomy of each bin after the binning process is finished. Homepage: https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://www.mathworks.com/products/compiler/mcr/ mcr/R2013a]
| align="center" | tools
| align="center" | [[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: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.mathworks.com/products/compiler/mcr/ mcr/R2013b]
| align="center" | tools
| align="center" | [[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: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.mathworks.com/products/compiler/mcr/ mcr/R2014a]
| align="center" | tools
| align="center" | [[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: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.mathworks.com/products/compiler/mcr/ mcr/R2014b]
| align="center" | tools
| align="center" | [[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: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.mathworks.com/products/compiler/mcr/ mcr/R2015a]
| align="center" | tools
| align="center" | [[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: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.mathworks.com/products/compiler/mcr/ mcr/R2015b]
| align="center" | tools
| align="center" | [[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: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.mathworks.com/products/compiler/mcr/ mcr/R2016a]
| align="center" | tools
| align="center" | [[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: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.mathworks.com/products/compiler/mcr/ mcr/R2016b]
| align="center" | tools
| align="center" | [[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: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.mathworks.com/products/compiler/mcr/ mcr/R2017a]
| align="center" | tools
| align="center" | [[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: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.mathworks.com/products/compiler/mcr/ mcr/R2017b]
| align="center" | tools
| align="center" | [[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: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.mathworks.com/products/compiler/mcr/ mcr/R2018a]
| align="center" | tools
| align="center" | [[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: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.mathworks.com/products/compiler/mcr/ mcr/R2018b]
| align="center" | tools
| align="center" | [[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: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools CC-Wiki: MATLAB<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/voutcn/megahit megahit/1.1.1]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. Homepage: https://github.com/voutcn/megahit Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 and cuda/8.0.44<br />'''Description:''' </div>
|-
| align="center" | [http://jgi.doe.gov/data-and-tools/meraculous/ meraculous/2.2.4]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' gcc/4.8.5<br />'''Description:''' </div>
|-
| align="center" | [https://bitbucket.org/berkeleylab/metabat metabat/2.12.1]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MetaBAT: A robust statistical framework for reconstructing genomes from metagenomic data Homepage: https://bitbucket.org/berkeleylab/metabat Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.sph.umich.edu/csg/abecasis/metal/ metal/2011-03-25]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://bitbucket.org/biobakery/metaphlan2 metaphlan/2.2.0]
| align="center" | bio
| align="center" |
| <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://bitbucket.org/biobakery/metaphlan2 Keyword:bio<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://glaros.dtc.umn.edu/gkhome/metis/metis/overview metis/4.0.3]
| align="center" | math
| align="center" |
| <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 Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://glaros.dtc.umn.edu/gkhome/metis/metis/overview metis/5.1.0]
| align="center" | math
| align="center" |
| <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 Keyword:math<br />'''Prerequisites:''' gcc/4.8.5 or gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://minia.genouest.org/ minia/2.0.7]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Minia is a short-read assembler based on a de Bruijn graph Homepage: http://minia.genouest.org/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://genome.sph.umich.edu/wiki/Minimac2 minimac2/2014.9.15]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://genome.sph.umich.edu/wiki/Minimac3 minimac3/2.0.1]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://mixcr.readthedocs.io/en/latest/quickstart.html mixcr/2.1.10]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://mixcr.readthedocs.io/en/latest/quickstart.html mixcr/2.1.5]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://01.org/mkl-dnn mkl-dnn/0.16]
| align="center" | ai
| align="center" |
| <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 />'''Prerequisites:''' gcc/7.3.0 or intel/2018.3<br />'''Description:''' </div>
|-
| align="center" | [http://www.cmbi.ru.nl/molden/ molden/5.7]
| align="center" | chem
| align="center" |
| <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/ Keyword:chem<br />'''Prerequisites:''' intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://mono-framework.com mono/4.6.2.7]
| align="center" | tools
| align="center" |
| <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: http://mono-framework.com Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.mono-project.com/ mono/5.4.0.56]
| align="center" | tools
| align="center" |
| <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: http://www.mono-project.com/ Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://www.mothur.org/ mothur/1.39.4]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.mothur.org/ mothur/1.40.4]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/jmp75/MPI.NET mpi.net/13-08-2017]
| align="center" | mpi
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MPI.NET is a high-performance, easy-to-use implementation of the Message Passing Interface (MPI) for Microsoft's .NET environment. Homepage: https://github.com/jmp75/MPI.NET Keyword:mpi<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [https://bitbucket.org/mpi4py/mpi4py mpi4py/2.0.0]
| align="center" | tools
| align="center" |
| <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 Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [https://bitbucket.org/mpi4py/mpi4py mpi4py/3.0.0]
| align="center" | tools
| align="center" |
| <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 Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0 and cuda/8.0.44 and openmpi/2.1.1 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://mrbayes.csit.fsu.edu mrbayes/3.2.6]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MrBayes is a program for the Bayesian estimation of phylogeny. - Homepage: http://mrbayes.csit.fsu.edu Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://sobereva.com/multiwfn/ multiwfn/3.5]
| align="center" | chem
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://mummer.sourceforge.net/ mummer-64bit/3.23]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://mummer.sourceforge.net/ mummer/3.23]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://mummer.sourceforge.net/ mummer/4.0.0beta2]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://www.mysql.com/ mysql/5.7]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MySQL is (as of March 2014) the world's second most widely used open-source relational database management system (RDBMS). Homepage: http://www.mysql.com/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.ks.uiuc.edu/Research/namd/ namd-mpi/2.12]
| align="center" | chem
| align="center" | [[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 CC-Wiki: NAMD<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.ks.uiuc.edu/Research/namd/ namd-multicore/2.12]
| align="center" | chem
| align="center" | [[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 CC-Wiki: NAMD<br />'''Prerequisites:''' intel/2016.4 or intel/2016.4 and cuda/8.0.44<br />'''Description:''' </div>
|-
| align="center" | [http://www.ks.uiuc.edu/Research/namd/ namd-verbs-smp/2.12]
| align="center" | chem
| align="center" | [[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 CC-Wiki: NAMD<br />'''Prerequisites:''' intel/2016.4 and cuda/8.0.44<br />'''Description:''' </div>
|-
| align="center" | [http://www.ks.uiuc.edu/Research/namd/ namd-verbs/2.12]
| align="center" | chem
| align="center" | [[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 CC-Wiki: NAMD<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://developer.nvidia.com/nccl nccl/2.3.5]
| align="center" | tools
| align="center" |
| <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 Keyword:tools<br />'''Prerequisites:''' gcc/7.3.0 and cuda/10.0.130<br />'''Description:''' </div>
|-
| align="center" | [http://www.ncl.ucar.edu ncl/6.4.0]
| align="center" | vis
| align="center" |
| <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 Keyword:vis<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://nco.sourceforge.net nco/4.6.6]
| align="center" | io
| align="center" |
| <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: http://nco.sourceforge.net Keyword:io<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://meteora.ucsd.edu/~pierce/ncview_home_page.html ncview/2.1.7]
| align="center" | vis
| align="center" |
| <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 Keyword:vis<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-c++-mpi/4.2]
| align="center" | io
| align="center" |
| <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 />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-c++/4.2]
| align="center" | io
| align="center" |
| <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 />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-c++4-mpi/4.3.0]
| align="center" | io
| align="center" |
| <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 />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-fortran-mpi/4.4.4]
| align="center" | io
| align="center" |
| <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 />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or gcc/6.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-fortran/4.4.4]
| align="center" | io
| align="center" |
| <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 />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-mpi/4.1.3]
| align="center" | io
| align="center" |
| <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 />'''Prerequisites:''' intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-mpi/4.4.1.1]
| align="center" | io
| align="center" |
| <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 />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or gcc/6.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf/4.4.1.1]
| align="center" | io
| align="center" |
| <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 />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://python.org/ networkx/1.1]
| align="center" | tools
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://python.org/ networkx/2.1]
| align="center" | tools
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://cibiv.github.io/NextGenMap/ nextgenmap/0.5.0]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NextGenMap (NGM) is a flexible and fast read mapping program that is more than twice as fast as BWA, while achieving a mapping sensitivity similar to Stampy or Bowtie2. Homepage: http://cibiv.github.io/NextGenMap/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or gcc/5.4.0 and cuda/8.0.44<br />'''Description:''' </div>
|-
| align="center" | [http://cibiv.github.io/NextGenMap/ nextgenmap/0.5.4]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NextGenMap (NGM) is a flexible and fast read mapping program that is more than twice as fast as BWA, while achieving a mapping sensitivity similar to Stampy or Bowtie2. Homepage: http://cibiv.github.io/NextGenMap/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 and cuda/8.0.44<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/mfumagalli/ngsTools ngstools/1.0.1]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://ab-initio.mit.edu/wiki/index.php/NLopt nlopt/2.4.2]
| align="center" | math
| align="center" |
| <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 Keyword:math<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.shoup.net/ntl/ ntl/11.3.0]
| align="center" | math
| align="center" |
| <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/ Keyword:math<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.nwchem-sw.org nwchem/6.6.revision27746]
| align="center" | chem
| align="center" |
| <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 Keyword:chem<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.oasys-software.com/dyna/en/ oasys-ls-dyna/14.1]
| align="center" | phys
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.gnu.org/software/octave/ octave/4.2.1]
| align="center" | tools
| align="center" |
| <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: http://www.gnu.org/software/octave/ Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://openbabel.org openbabel/2.4.1]
| align="center" | chem
| align="center" |
| <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: http://openbabel.org Keyword:chem<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://xianyi.github.com/OpenBLAS/ openblas/0.2.20]
| align="center" | math
| align="center" |
| <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://xianyi.github.com/OpenBLAS/ Keyword:math<br />'''Prerequisites:''' gcc/6.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://opencolorio.org/ opencolorio/1.0.9]
| align="center" | vis
| align="center" |
| <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/ Keyword:vis<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://opencv.org/ opencv/2.4.13.3]
| align="center" | vis
| align="center" |
| <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 />'''Prerequisites:''' gcc/5.4.0 or gcc/5.4.0 and cuda/8.0.44<br />'''Description:''' </div>
|-
| align="center" | [http://opencv.org/ opencv/3.3.0]
| align="center" | vis
| align="center" |
| <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 />'''Prerequisites:''' gcc/5.4.0 or gcc/5.4.0 and cuda/8.0.44<br />'''Description:''' </div>
|-
| align="center" | [http://www.openexr.com/ openexr/2.2.1]
| align="center" | vis
| align="center" |
| <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: http://www.openexr.com/ Keyword:vis<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://www.openfoam.com/ openfoam/2.3.1]
| align="center" | phys
| align="center" | [[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: http://www.openfoam.com/ Keyword:phys CC-Wiki: OpenFOAM<br />'''Prerequisites:''' gcc/4.8.5 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.openfoam.com/ openfoam/3.0.1]
| align="center" | phys
| align="center" | [[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: http://www.openfoam.com/ Keyword:phys CC-Wiki: OpenFOAM<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.openfoam.org/ openfoam/4.1]
| align="center" | phys
| align="center" | [[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: http://www.openfoam.org/ Keyword:phys CC-Wiki: OpenFOAM<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.openfoam.org/ openfoam/5.0]
| align="center" | phys
| align="center" | [[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: http://www.openfoam.org/ Keyword:phys CC-Wiki: OpenFOAM<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://openimageio.org/ openimageio/1.8.7]
| align="center" | vis
| align="center" |
| <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: http://openimageio.org/ Keyword:vis<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://www.open-mpi.org/ openmpi/1.6.5]
| align="center" | mpi
| align="center" | [[MPI]]
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Open MPI Project is an open source MPI-2 implementation. Homepage: http://www.open-mpi.org/ Keyword:mpi CC-Wiki: MPI<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.open-mpi.org/ openmpi/1.8.8]
| align="center" | mpi
| align="center" | [[MPI]]
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Open MPI Project is an open source MPI-2 implementation. Homepage: http://www.open-mpi.org/ Keyword:mpi CC-Wiki: MPI<br />'''Prerequisites:''' gcc/4.8.5 or gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.open-mpi.org/ openmpi/2.0.2]
| align="center" | mpi
| align="center" | [[MPI]]
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Open MPI Project is an open source MPI-2 implementation. Homepage: http://www.open-mpi.org/ Keyword:mpi CC-Wiki: MPI<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2016.4 and cuda/8.0.44 or intel/2017.1 or pgi/17.3<br />'''Description:''' </div>
|-
| align="center" | [http://www.open-mpi.org/ openmpi/2.1.1]
| align="center" | mpi
| align="center" | [[MPI]]
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Open MPI Project is an open source MPI-2 implementation. Homepage: http://www.open-mpi.org/ Keyword:mpi CC-Wiki: MPI<br />'''Prerequisites:''' gcc/4.8.5 or gcc/5.4.0 or gcc/5.4.0 and cuda/8.0.44 or gcc/5.4.0 and cuda/9.0.176 or gcc/6.4.0 or gcc/6.4.0 and cuda/9.0.176 or intel/2016.4 or intel/2016.4 and cuda/8.0.44 or intel/2016.4 and cuda/9.0.176 or intel/2017.1 or pgi/13.10 or pgi/17.3<br />'''Description:''' </div>
|-
| align="center" | [http://www.open-mpi.org/ openmpi/3.1.2]
| align="center" | mpi
| align="center" | [[MPI]]
| <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: http://www.open-mpi.org/ Keyword:mpi CC-Wiki: MPI<br />'''Prerequisites:''' gcc/7.3.0 or gcc/7.3.0 and cuda/10.0.130<br />'''Description:''' </div>
|-
| align="center" | [http://code.google.com/p/openpgm/ openpgm/5.2.122]
| align="center" | tools
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://cec.mpg.de/forum/ orca/4.0.0.2]
| align="center" | chem
| align="center" | [[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/ Keyword:chem CC-Wiki: ORCA<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.0.2<br />'''Description:''' </div>
|-
| align="center" | [http://cec.mpg.de/forum/ orca/4.0.1.2]
| align="center" | chem
| align="center" | [[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/ Keyword:chem CC-Wiki: ORCA<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.0.2<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/wwood/OrfM orfm/0.7.1]
| align="center" | -
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://orthomcl.org/ orthomcl/2.0.9]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/imageworks/OpenShadingLanguage osl/1.9.6]
| align="center" | vis
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Advanced shading language for production GI renderers Homepage: https://github.com/imageworks/OpenShadingLanguage Keyword:vis<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://mvapich.cse.ohio-state.edu/benchmarks/ osu-micro-benchmarks/5.3.2]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OSU Micro-Benchmarks Homepage: http://mvapich.cse.ohio-state.edu/benchmarks/ Keyword:tools<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.p4est.org/ p4est/1.1]
| align="center" | math
| align="center" |
| <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/ Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://icl.cs.utk.edu/projects/papi/ papi/5.6.0]
| align="center" | tools
| align="center" |
| <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: http://icl.cs.utk.edu/projects/papi/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://savannah.gnu.org/projects/parallel/ parallel/20160722]
| align="center" | tools
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.paraview.org paraview-offscreen-gpu/5.4.0]
| align="center" | vis
| align="center" | [[Visualization]]
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ParaView is a scientific parallel visualizer. Homepage: http://www.paraview.org Keyword:vis CC-Wiki: Visualization<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.paraview.org paraview-offscreen/5.3.0]
| align="center" | vis
| align="center" | [[Visualization]]
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ParaView is a scientific parallel visualizer. Homepage: http://www.paraview.org Keyword:vis CC-Wiki: Visualization<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.paraview.org paraview/5.3.0]
| align="center" | vis
| align="center" | [[Visualization]]
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ParaView is a scientific parallel visualizer. Homepage: http://www.paraview.org Keyword:vis CC-Wiki: Visualization<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview parmetis/4.0.3]
| align="center" | math
| align="center" |
| <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 />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://pointclouds.org/ pcl/1.8.1]
| align="center" | math
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Point Cloud Library (PCL) is a standalone, large scale, open project for 2D/3D image and point cloud processing. Homepage: http://pointclouds.org/ Keyword:math<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://www.pcre.org/ pcre/8.39]
| align="center" | -
| align="center" |
| <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: http://www.pcre.org/<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.pcre.org/ pcre2/10.31]
| align="center" | -
| align="center" |
| <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: http://www.pcre.org/<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://sco.h-its.org/exelixis/web/software/pear/ pear/0.9.10]
| align="center" | bio
| align="center" |
| <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: http://sco.h-its.org/exelixis/web/software/pear/ Keyword:bio<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://penncnv.openbioinformatics.org/en/latest/ penncnv/1.0.4]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PennCNV is 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: http://penncnv.openbioinformatics.org/en/latest/ Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://penncnv.openbioinformatics.org/en/latest/ penncnv/1.0.5]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PennCNV is 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: http://penncnv.openbioinformatics.org/en/latest/ Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.perl.org/ perl/5.16.3]
| align="center" | tools
| align="center" | [[Perl]]
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Larry Wall's Practical Extraction and Report Language Homepage: http://www.perl.org/ Extensions: AnyEvent-7.04, B::LintSubs-0.06, Bio::Perl-1.6.901, boolean-0.30, Class::Load-0.20, Class::Singleton-1.4, Data::OptList-0.107, Data::Stag-0.11, Data::Types-0.09, DateTime-1.01, DateTime::Locale-0.45, DateTime::TimeZone-1.58, DateTime::Tiny-1.04, DB_File-1.827, DBI-1.625, Devel::GlobalDestruction-0.11, Dist::CheckConflicts-0.02, Eval::Closure-0.08, File::Slurp-9999.19, HTML::Entities-3.70, HTML::Tagset-3.20, HTTP::Date-6.02, HTTP::Request-6.06, IO::HTML-1.00, IO::String-1.08, IO::Tty-1.10, IPC::Run-0.92, List::MoreUtils-0.33, LWP::MediaTypes-6.02, Module::Implementation-0.06, Module::Runtime-0.013, Moose-2.0801, Mouse-1.05, MRO::Compat-0.12, Package::DeprecationManager-0.13, Package::Stash-0.34, Params::Util-1.07, Params::Validate-1.07, Sub::Exporter-0.985, Sub::Exporter::Progressive-0.001010, Sub::Install-0.926, Sub::Name-0.05, Sub::Uplevel-0.24, Test::Exception-0.31, Test::Fatal-0.010, Test::Harness-3.28, Test::Output-1.01, Test::Requires-0.06, Test::Simple-0.98, Test::Tester-0.108, Test::Warn-0.24, Tie::IxHash-1.23, Tree::DAG_Node-1.11, Try::Tiny-0.12, URI-1.60, XML::NamespaceSupport-1.11, XML::SAX-0.99, XML::SAX::Base-1.08 Keyword:tools CC-Wiki: Perl<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://www.perl.org/ perl/5.22.2]
| align="center" | tools
| align="center" | [[Perl]]
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Perl 5 is a highly capable, feature-rich programming language with over 29 years of development. Homepage: https://www.perl.org/ Keyword:tools CC-Wiki: Perl<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.perl.org/ perl/5.22.4]
| align="center" | tools
| align="center" | [[Perl]]
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Larry Wall's Practical Extraction and Report Language Homepage: http://www.perl.org/ Extensions: Acme::Damn-0.08, Algorithm::Dependency-1.110, Algorithm::Diff-1.1903, aliased-0.34, AnyData-0.12, AnyEvent-7.12, AppConfig-1.71, Archive::Extract-0.76, Authen::SASL-2.16, B::Lint-1.20, Bit::Vector-7.4, boolean-0.45, Bundle::BioPerl-2.1.9, Canary::Stability-2011, Capture::Tiny-0.40, Carp-1.38, Class::Accessor-0.34, Class::Data::Inheritable-0.08, Class::DBI-3.0.17, Class::DBI::SQLite-0.11, Class::Inspector-1.28, Class::ISA-0.36, Class::Load-0.23, Class::Load::XS-0.09, Class::Singleton-1.5, Class::Trigger-0.14, Clone-0.38, Config::General-2.61, CPANPLUS-0.9160, Crypt::DES-2.07, Crypt::Rijndael-1.13, Cwd::Guard-0.05, Data::Dumper::Concise-2.022, Data::Grove-0.08, Data::OptList-0.110, Data::Section::Simple-0.07, Data::Stag-0.14, Data::Types-0.09, Data::UUID-1.221, Date::Handler-1.2, Date::Language-2.30, DateTime-1.28, DateTime::Locale-1.03, DateTime::TimeZone-1.98, DateTime::Tiny-1.04, DBD::AnyData-0.110, DBD::SQLite-1.50, DBI-1.636, DBIx::Admin::TableInfo-3.01, DBIx::ContextualFetch-1.03, DBIx::Simple-1.35, Devel::CheckCompiler-0.06, Devel::GlobalDestruction-0.13, Devel::StackTrace-2.01, Digest::HMAC-1.03, Digest::SHA1-2.13, Dist::CheckConflicts-0.11, Email::Date::Format-1.005, Encode::Locale-1.05, Error-0.17024, Eval::Closure-0.13, Exception::Class-1.40, Expect-1.32, Exporter-5.72, Exporter::Declare-0.114, Exporter::Tiny-0.042, ExtUtils::Config-0.008, ExtUtils::Helpers-0.022, ExtUtils::InstallPaths-0.011, ExtUtils::MakeMaker-7.18, Fennec::Lite-0.004, File::CheckTree-4.42, File::Copy::Recursive-0.38, File::Find::Rule-0.34, File::Find::Rule::Perl-1.15, File::HomeDir-1.00, File::Listing-6.04, File::ShareDir::Install-0.11, File::Slurp-9999.19, File::Slurp::Tiny-0.004, File::Spec-3.62, File::Which-1.21, Font::TTF-1.05, forks-0.36, FreezeThaw-0.5001, GD-2.68, GD::Graph-1.52, Getopt::Long-2.48, Git-0.41, GO-0.04, GO::Utils-0.15, Graph-0.9704, Hash::Merge-0.200, HTML::Entities::Interpolate-1.09, HTML::Form-6.03, HTML::Parser-3.72, HTML::Tagset-3.20, HTML::Tree-5.03, HTTP::Cookies-6.01, HTTP::Daemon-6.01, HTTP::Date-6.02, HTTP::Negotiate-6.01, HTTP::Request-6.11, HTTP::Tiny-0.058, Ima::DBI-0.35, Import::Into-1.002005, Inline-0.80, Inline::C-0.78, IO::All-0.87, IO::HTML-1.001, IO::Socket::SSL-2.027, IO::String-1.08, IO::Stringy-2.111, IO::Tty-1.12, IPC::Run-0.94, IPC::Run3-0.048, JSON-2.90, Lingua::EN::PluralToSingular-0.18, List::AllUtils-0.10, List::MoreUtils-0.415, Log::Handler-0.84, Log::Message-0.08, Log::Message::Simple-0.10, LWP::MediaTypes-6.02, LWP::Simple-6.15, Mail::Util-2.18, Math::Bezier-0.01, Math::Round-0.07, Math::VecStat-0.08, Meta::Builder-0.003, MIME::Lite-3.030, MIME::Types-2.13, Mock::Quick-1.110, Module::Build-0.4218, Module::Build::Tiny-0.039, Module::Build::XSUtil-0.16, Module::Implementation-0.09, Module::Pluggable-5.2, Module::Runtime-0.014, Moo-2.001001, Moose-2.1801, Mouse-v2.4.5, MRO::Compat-0.12, Net::HTTP-6.09, Net::SMTP::SSL-1.03, Net::SNMP-v6.0.1, Number::Compare-0.03, Number::Format-1.75, Object::Accessor-0.48, Package::DeprecationManager-0.16, Package::Stash-0.37, Package::Stash::XS-0.28, Params::Util-1.07, Params::Validate-1.24, Parse::RecDescent-1.967013, Perl::Unsafe::Signals-0.03, Pod::LaTeX-0.61, Pod::Plainer-1.04, Pod::POM-2.01, Readonly-2.04, Regexp::Common-2016020301, Scalar::Util-1.45, Set::Array-0.30, Set::IntSpan-1.19, Set::IntSpan::Fast-1.15, Set::Scalar-1.29, Shell-0.73, SQL::Abstract-1.81, SQL::Statement-1.410, Statistics::Basic-1.6611, Statistics::Descriptive-3.0612, strictures-2.000003, Sub::Exporter-0.987, Sub::Exporter::Progressive-0.001011, Sub::Install-0.928, Sub::Name-0.15, Sub::Uplevel-0.25, Sub::Uplevel-0.25, SVG-2.77, Switch-2.17, Sys::SigAction-0.23, Template-2.26, Template::Plugin::Number::Format-1.06, Term::ReadKey-2.33, Term::UI-0.46, Test::ClassAPI-1.06, Test::Deep-1.120, Test::Differences-0.64, Test::Exception-0.43, Test::Exception::LessClever-0.006, Test::Fatal-0.014, Test::Harness-3.36, Test::LeakTrace-0.15, Test::Most-0.34, Test::NoWarnings-1.04, Test::Output-1.03, Test::Pod-1.51, Test::Requires-0.10, Test::Simple-1.302019, Test::Version-2.03, Test::Warn-0.30, Test::Warnings-0.026, Text::Balanced-2.03, Text::CSV-1.33, Text::Diff-1.44, Text::Format-0.59, Text::Glob-0.09, Text::Iconv-1.7, Text::Soundex-3.05, Text::Table-1.130, Tie::Function-0.02, Tie::IxHash-1.23, Time::HiRes-1.9754, Time::Piece-1.31, Time::Piece::MySQL-0.06, Tree::DAG_Node-1.29, Try::Tiny-0.24, UNIVERSAL::moniker-0.08, URI-1.71, version-0.9916, Want-0.29, WWW::RobotRules-6.02, XML::Bare-0.53, XML::DOM-1.46, XML::LibXML-2.0132, XML::NamespaceSupport-1.11, XML::SAX-0.99, XML::SAX-1.00, XML::SAX::Base-1.08, XML::SAX::Writer-0.56, XML::Simple-2.22, XML::Tiny-2.06, XML::Twig-3.49, XML::Writer-0.625, XML::XPath-1.36 Keyword:tools CC-Wiki: Perl<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://metacpan.org/pod/Perl4::CoreLibs perl4-corelibs/0.003]
| align="center" | tools
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.mcs.anl.gov/petsc petsc-64bits/3.7.5]
| align="center" | tools
| align="center" |
| <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 Keyword:tools<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.mcs.anl.gov/petsc petsc-debug/3.8.2]
| align="center" | tools
| align="center" |
| <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 Keyword:tools<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.mcs.anl.gov/petsc petsc/3.7.5]
| align="center" | tools
| align="center" |
| <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 Keyword:tools<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.mcs.anl.gov/petsc petsc/3.8.2]
| align="center" | tools
| align="center" |
| <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 Keyword:tools<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.pgroup.com/ pgi/13.10]
| align="center" | tools
| align="center" |
| <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/<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.pgroup.com/ pgi/17.3]
| align="center" | tools
| align="center" |
| <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/<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://samtools.github.io/hts-specs) picard/2.1.1]
| align="center" | bio
| align="center" |
| <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 (http://samtools.github.io/hts-specs) format. - Homepage: http://broadinstitute.github.io/picard/ Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://samtools.github.io/hts-specs) picard/2.10.7]
| align="center" | bio
| align="center" |
| <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 (http://samtools.github.io/hts-specs) format. Homepage: http://broadinstitute.github.io/picard/ Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://samtools.github.io/hts-specs) picard/2.17.3]
| align="center" | bio
| align="center" |
| <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 (http://samtools.github.io/hts-specs) format. Homepage: http://broadinstitute.github.io/picard/ Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://samtools.github.io/hts-specs) picard/2.18.9]
| align="center" | bio
| align="center" |
| <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 (http://samtools.github.io/hts-specs) format. Homepage: http://broadinstitute.github.io/picard/ Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/broadinstitute/pilon pilon/1.22]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Pilon is an automated genome assembly improvement and variant detection tool To run pilon, please use: java -jar $EBROOTPILON/pilon-1.22.jar ... Use -Xmx Java option to adjust memory as in: java -Xmx8G -jar $EBROOTPILON/pilon-1.22.jar ... Homepage: https://github.com/broadinstitute/pilon Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://pngu.mgh.harvard.edu/~purcell/plink/ plink/1.07]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://www.cog-genomics.org/plink/1.9/ plink/1.9b_4.1-x86_64]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: plink-1.9-x86_64: Whole-genome association analysis toolset Homepage: https://www.cog-genomics.org/plink/1.9/ Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://www.cog-genomics.org/plink/1.9/ plink/1.9b_5.2-x86_64]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: plink-1.9-x86_64: Whole-genome association analysis toolset Homepage: https://www.cog-genomics.org/plink/1.9/ Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.plumed-code.org plumed/2.3.0]
| align="center" | chem
| align="center" |
| <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: http://www.plumed-code.org Keyword:chem<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.plumed-code.org plumed/2.3.2]
| align="center" | chem
| align="center" |
| <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: http://www.plumed-code.org Keyword:chem<br />'''Prerequisites:''' intel/2016.4 and cuda/8.0.44 and openmpi/2.0.2 or intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [https://trac.mcs.anl.gov/projects/parallel-netcdf pnetcdf/1.8.1]
| align="center" | io
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PnetCDF is a high-performance parallel I/O library for accessing files in format compatibility with Unidata's NetCDF, specifically the formats of CDF-1, 2, and 5. The CDF-5 file format, an extension of CDF-2, supports unsigned data types and uses 64-bit integers to allow users to define large dimensions, attributes, and variables (&gt; 2B array elements). Homepage: https://trac.mcs.anl.gov/projects/parallel-netcdf Keyword:io<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [https://www.postgresql.org/ postgresql/10.2]
| align="center" | tools
| align="center" |
| <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/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://www.postgresql.org/ postgresql/9.6.6]
| align="center" | tools
| align="center" |
| <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/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://matsen.fhcrc.org/pplacer/ pplacer/1.1.alpha19]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis. Homepage: http://matsen.fhcrc.org/pplacer/ Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://prinseq.sourceforge.net prinseq/0.20.4]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://prodigal.ornl.gov/ prodigal/2.6.3]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Homepage: http://prodigal.ornl.gov/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://trac.osgeo.org/proj/ proj/4.9.3]
| align="center" | geo
| align="center" |
| <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: http://trac.osgeo.org/proj/ Keyword:geo<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/google/protobuf/ protobuf/3.3.0]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Google Protocol Buffers Homepage: https://github.com/google/protobuf/ Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [https://pypy.org/index.html pypy/5.8]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PyPy is a fast, compliant alternative implementation of the Python language (2.7.13 and 3.5.3). Homepage: https://pypy.org/index.html Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://python.org/ python/2.7.13]
| align="center" | tools
| align="center" | [[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: http://python.org/ Keyword:tools CC-Wiki: Python<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://python.org/ python/2.7.14]
| align="center" | tools
| align="center" | [[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: http://python.org/ Extensions: pip-18.1, pysqlite-2.8.3, readline-6.2.4.1, setuptools-40.6.3, virtualenv-16.1.0, wheel-0.32.3 Keyword:tools CC-Wiki: Python<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://python.org/ python/3.5.2]
| align="center" | tools
| align="center" | [[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: http://python.org/ Keyword:tools CC-Wiki: Python<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://python.org/ python/3.5.4]
| align="center" | tools
| align="center" | [[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: http://python.org/ Extensions: pip-18.1, readline-6.2.4.1, setuptools-40.6.3, virtualenv-16.1.0, wheel-0.32.3 Keyword:tools CC-Wiki: Python<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://python.org/ python/3.6.3]
| align="center" | tools
| align="center" | [[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: http://python.org/ Extensions: pip-18.1, readline-6.2.4.1, setuptools-40.6.3, virtualenv-16.1.0, wheel-0.32.3 Keyword:tools CC-Wiki: Python<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://python.org/ python/3.7.0]
| align="center" | tools
| align="center" | [[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: http://python.org/ Extensions: gnureadline-6.3.8, pip-18.1, setuptools-40.6.3, virtualenv-16.1.0, wheel-0.32.3 Keyword:tools CC-Wiki: Python<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://bitbucket.org/mpi4py/mpi4py python27-mpi4py/2.0.0]
| align="center" | tools
| align="center" |
| <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 Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://python.org/ python27-scipy-stack/2017a]
| align="center" | math
| align="center" |
| <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/ Extensions: arff-2.1.0, backports.shutil_get_terminal_size-1.0.0, backports_abc-0.4, bitstring-3.1.5, blist-1.3.6, certifi-2016.8.8, cryptography-1.7.1, Cycler-0.10.0, Cython-0.25.2, dateutil-2.6.0, deap-1.0.2, decorator-4.0.10, ecdsa-0.13, enum34-1.1.6, funcsigs-1.0.2, functools32-3.2.3-2, ipykernel-4.4.1, ipython-5.1.0, ipython_genutils-0.1.0, ipywidgets-5.2.2, Jinja2-2.8, jsonschema-2.5.1, jupyter_client-4.3.0, jupyter_core-4.1.1, lockfile-0.12.2, MarkupSafe-0.23, matplotlib-1.5.3, mistune-0.7.3, mock-2.0.0, mpmath-0.19, nbformat-4.1.0, netaddr-0.7.18, netifaces-0.10.5, nose-1.3.7, notebook-4.2.2, numpy-1.12.0, pandas-0.19.2, paramiko-2.1.1, path.py-10.0, pathlib2-2.1.0, paycheck-1.0.2, pbr-1.10.0, pexpect-4.2.0, pickleshare-0.7.4, prompt_toolkit-1.0.9, ptyprocess-0.5.1, pycrypto-2.6.1, Pygments-2.1.3, pyparsing-2.1.10, pysqlite-2.8.3, pytz-2016.10, PyZMQ-16.0.2, requests-2.11.0, scipy-0.18.1, setuptools-32.3.1, simplegeneric-0.8.1, singledispatch-3.4.0.3, six-1.10.0, sympy-1.0, terminado-0.6, tornado-4.4.1, traitlets-4.2.2, widgetsnbextension-1.2.6 Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [https://bitbucket.org/mpi4py/mpi4py python35-mpi4py/2.0.0]
| align="center" | tools
| align="center" |
| <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 Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://python.org/ python35-scipy-stack/2017a]
| align="center" | math
| align="center" |
| <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/ Extensions: arff-2.1.0, backports.shutil_get_terminal_size-1.0.0, bitstring-3.1.5, blist-1.3.6, certifi-2016.8.8, cryptography-1.7.1, Cycler-0.10.0, Cython-0.25.2, dateutil-2.6.0, deap-1.0.2, decorator-4.0.10, ecdsa-0.13, enum34-1.1.6, funcsigs-1.0.2, ipykernel-4.4.1, ipython-5.1.0, ipython_genutils-0.1.0, ipywidgets-5.2.2, Jinja2-2.8, jsonschema-2.5.1, jupyter_client-4.3.0, jupyter_core-4.1.1, lockfile-0.12.2, MarkupSafe-0.23, matplotlib-1.5.3, mistune-0.7.3, mock-2.0.0, mpmath-0.19, nbformat-4.1.0, netaddr-0.7.18, netifaces-0.10.5, nose-1.3.7, notebook-4.2.2, numpy-1.12.0, pandas-0.19.2, paramiko-2.1.1, path.py-10.0, pathlib2-2.1.0, paycheck-1.0.2, pbr-1.10.0, pexpect-4.2.0, pickleshare-0.7.4, prompt_toolkit-1.0.9, ptyprocess-0.5.1, pycrypto-2.6.1, Pygments-2.1.3, pyparsing-2.1.10, pytz-2016.10, PyZMQ-16.0.2, requests-2.11.0, scipy-0.18.1, setuptools-32.3.1, simplegeneric-0.8.1, singledispatch-3.4.0.3, six-1.10.0, sympy-1.0, terminado-0.6, tornado-4.4.1, traitlets-4.2.2, widgetsnbextension-1.2.6 Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.qhull.org qhull/2015.2]
| align="center" | math
| align="center" |
| <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 Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://qjson.sourceforge.net/ qjson/0.9.0]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: QJson is a Qt-based library that maps JSON data to QVariant objects and vice versa. Homepage: http://qjson.sourceforge.net/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://sourceforge.net/projects/qrupdate/ qrupdate/1.1.2]
| align="center" | math
| align="center" |
| <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 />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [https://www.riverbankcomputing.com/software/qscintilla qscintilla/2.10.7]
| align="center" | tools
| align="center" |
| <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 Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://qt.io/ qt/3.3.8]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Qt is a comprehensive cross-platform C++ application framework. Homepage: http://qt.io/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://qt.io/ qt/4.8.7]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Qt is a comprehensive cross-platform C++ application framework. Homepage: http://qt.io/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://qt.io/ qt/5.10.1]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Qt is a comprehensive cross-platform C++ application framework. Homepage: http://qt.io/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://qt.io/ qt/5.11.3]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Qt is a comprehensive cross-platform C++ application framework. Homepage: http://qt.io/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://qt.io/ qt/5.6.1]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Qt is a comprehensive cross-platform C++ application framework. Homepage: http://qt.io/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://qt.io/ qt/5.9.6]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Qt is a comprehensive cross-platform C++ application framework. Homepage: http://qt.io/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.pwscf.org/ quantumespresso/6.0]
| align="center" | chem
| align="center" | [[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: http://www.pwscf.org/ Keyword:chem CC-Wiki: Quantum ESPRESSO<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.pwscf.org/ quantumespresso/6.1]
| align="center" | chem
| align="center" | [[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: http://www.pwscf.org/ Keyword:chem CC-Wiki: Quantum ESPRESSO<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.pwscf.org/ quantumespresso/6.3]
| align="center" | chem
| align="center" | [[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: http://www.pwscf.org/ Keyword:chem CC-Wiki: Quantum ESPRESSO<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.r-project.org/ r-bundle-bioconductor/3.4]
| align="center" | bio
| align="center" |
| <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: http://www.r-project.org/ Extensions: abind-1.4-5, acepack-1.4.1, ade4-1.7-6, affy-1.52.0, affycoretools-1.46.5, affyio-1.44.0, AgiMicroRna-2.24.0, ALDEx2-1.6.0, annaffy-1.46.0, annotate-1.52.1, AnnotationDbi-1.36.2, AnnotationForge-1.16.1, AnnotationHub-2.6.5, ape-4.1, assertthat-0.2.0, assertthat-0.2.0, backports-1.1.0, base64-2.0, base64enc-0.1-3, baySeq-2.8.0, beanplot-1.2, BH-1.62.0-1, BiasedUrn-1.07, bindr-0.1, bindrcpp-0.2, Biobase-2.34.0, BiocGenerics-0.20.0, BiocInstaller-1.24.0, BiocParallel-1.8.2, biomaRt-2.30.0, biomformat-1.2.0, Biostrings-2.42.1, biovizBase-1.22.0, bit-1.1-12, bit64-0.9-7, bitops-1.0-6, blob-1.1.0, BSgenome-1.42.0, BSgenome.Hsapiens.UCSC.hg19-1.4.0, bumphunter-1.14.0, Category-2.40.0, caTools-1.17.1, CGHbase-1.34.0, checkmate-1.8.2, clusterRepro-0.5-1.1, coin-1.2-0, colorspace-1.3-2, corpcor-1.6.9, cummeRbund-2.16.0, curl-2.7, dada2-1.2.2, data.table-1.10.4, DBI-0.7, DEGseq-1.28.0, DEoptimR-1.0-8, derfinder-1.8.5, derfinderHelper-1.8.1, DESeq2-1.14.1, dichromat-2.0-0, digest-0.6.12, digest-0.6.12, diptest-0.75-7, doParallel-1.0.10, doRNG-1.6.6, dplyr-0.7.1, DynDoc-1.52.0, edgeR-3.16.5, ellipse-0.3-8, ensembldb-1.6.2, evaluate-0.10.1, fastcluster-1.1.22, FDb.InfiniumMethylation.hg19-2.2.0, ff-2.2-13, flexmix-2.3-14, foreach-1.4.3, Formula-1.2-1, fpc-2.1-10, futile.logger-1.4.3, futile.logger-1.4.3, futile.logger-1.4.3, futile.options-1.0.0, futile.options-1.0.0, futile.options-1.0.0, gcrma-2.46.0, gdata-2.18.0, gdsfmt-1.10.1, genefilter-1.56.0, geneLenDataBase-1.10.0, geneplotter-1.52.0, GenomeGraphs-1.34.0, GenomeInfoDb-1.10.3, GenomicAlignments-1.10.1, GenomicFeatures-1.26.4, GenomicFiles-1.10.3, GenomicRanges-1.26.4, genoset-1.30.0, GEOquery-2.40.0, GGally-1.3.1, ggbio-1.22.4, ggplot2-2.2.1, glmnet-2.0-10, glue-1.1.1, GO.db-3.4.0, goseq-1.26.0, GOstats-2.40.0, gplots-3.0.1, graph-1.52.0, gridBase-0.4-7, gridExtra-2.2.1, GSEABase-1.36.0, gtable-0.2.0, gtools-3.5.0, Gviz-1.18.2, HCsnip-1.14.0, hgu133plus2.db-3.2.3, highr-0.6, Hmisc-4.0-3, Homo.sapiens-1.3.1, htmlTable-1.9, htmltools-0.3.6, htmlwidgets-0.8, httpuv-1.3.3, httr-1.2.1, hwriter-1.3.2, igraph-1.0.1, illuminaio-0.16.0, impute-1.48.0, interactiveDisplayBase-1.12.0, IRanges-2.8.2, irlba-2.2.1, iterators-1.0.8, jsonlite-1.5, KEGG.db-3.2.3, KEGGgraph-1.32.0, KEGGprofile-1.16.0, KEGGREST-1.14.1, kernlab-0.9-25, knitr-1.16, labeling-0.3, lambda.r-1.1.9, lambda.r-1.1.9, lambda.r-1.1.9, latticeExtra-0.6-28, lazyeval-0.2.0, limma-3.30.13, locfit-1.5-9.1, logspline-2.1.9, lumi-2.26.4, magrittr-1.5, markdown-0.8, marray-1.52.0, maSigPro-1.46.0, matrixStats-0.52.2, mclust-5.3, memoise-1.1.0, metagenomeSeq-1.16.0, methylumi-2.20.0, mime-0.5, minfi-1.20.2, mixOmics-6.1.1, mixOmics-6.1.3, modeltools-0.2-21, multcomp-1.4-6, multtest-2.30.0, munsell-0.4.3, mvtnorm-1.0-6, nleqslv-3.3, NMF-0.20.6, NOISeq-2.18.0, nor1mix-1.2-2, oligoClasses-1.36.0, openssl-0.9.6, org.Hs.eg.db-3.4.0, OrganismDbi-1.16.0, pcaMethods-1.66.0, penalized-0.9-50, perm-1.0-0.0, perm-1.0-0.0, permute-0.9-4, PFAM.db-3.4.0, phyloseq-1.19.1, pkgconfig-2.0.1, pkgmaker-0.22, plogr-0.1-1, plyr-1.8.4, png-0.1-7, polyester-1.10.1, prabclus-2.2-6, preprocessCore-1.36.0, prettyunits-1.0.2, progress-1.1.2, quadprog-1.5-5, qvalue-2.6.0, R.methodsS3-1.7.1, R.oo-1.21.0, R.utils-2.5.0, R6-2.2.2, randomForestSRC-2.4.2, RBGL-1.50.0, RColorBrewer-1.1-2, Rcpp-0.12.11, RcppArmadillo-0.7.900.2.0, RcppParallel-4.3.20, RCurl-1.95-4.5, registry-0.3, ReportingTools-2.14.0, reshape-0.8.6, reshape2-1.4.2, rgl-0.98.1, Rgraphviz-2.18.0, rhdf5-2.18.0, rlang-0.1.1, RNASeqPower-1.14.0, rngtools-1.2.4, robustbase-0.92-7, Rsamtools-1.26.2, RSQLite-2.0, Rsubread-1.24.2, rtracklayer-1.34.2, S4Vectors-0.12.2, samr-2.0, sandwich-2.3-4, scales-0.4.1, shiny-1.0.3, ShortRead-1.32.1, sigaR-1.22.0, siggenes-1.48.0, sm-2.2-5.4, snow-0.4-2, snowfall-1.84-6.1, SNPRelate-1.8.0, sourcetools-0.1.6, SPIA-2.26.0, stringi-1.1.5, stringr-1.2.0, SummarizedExperiment-1.4.0, TeachingDemos-2.10, TH.data-1.0-8, tibble-1.3.3, tidyr-0.6.3, trimcluster-0.1-2, TxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2, VariantAnnotation-1.20.3, vegan-2.4-3, venn-1.2, viridis-0.4.0, viridisLite-0.2.0, XML-3.98-1.9, xtable-1.8-2, xtable-1.8-2, XVector-0.14.1, yaml-2.1.14, zlibbioc-1.20.0, zoo-1.8-0 Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://www.r-project.org/ r/3.3.3]
| align="center" | tools
| align="center" | [[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: http://www.r-project.org/ Keyword:tools CC-Wiki: R<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.r-project.org/ r/3.4.0]
| align="center" | tools
| align="center" | [[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: http://www.r-project.org/ Keyword:tools CC-Wiki: R<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.r-project.org/ r/3.4.3]
| align="center" | tools
| align="center" | [[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: http://www.r-project.org/ Keyword:tools CC-Wiki: R<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.r-project.org/ r/3.5.0]
| align="center" | tools
| align="center" | [[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: http://www.r-project.org/ Keyword:tools CC-Wiki: R<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/isovic/racon/ racon/20170719]
| align="center" | bio
| align="center" |
| <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/isovic/racon/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/zorino/ray ray/3.0.0]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/1.8.8 or intel/2016.4 and openmpi/1.8.8<br />'''Description:''' </div>
|-
| align="center" | [http://eddylab.org/software/recon/ recon/1.08]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/rlabduke/reduce reduce/20180820]
| align="center" | -
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page relion/2.1.0]
| align="center" | chem
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). Homepage: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Keyword:chem<br />'''Prerequisites:''' intel/2016.4 and cuda/8.0.44 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/TACC/remora remora/1.8.2]
| align="center" | tools
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://repast.github.io/ repasthpc/2.2.0]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation platforms that have collectively been under continuous development for over 15 years: Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based modeling system that is designed for use on large computing clusters and supercomputers. - Homepage: https://repast.github.io/ Keyword:bio<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [https://bix.ucsd.edu/repeatscout/ repeatscout/1.0.5]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RepeatScout is a tool to discover repetitive substrings in DNA. Homepage: https://bix.ucsd.edu/repeatscout/ Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer rnammer/1.2]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RNAmmer 1.2 predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences. The method is described in detail in the following article: RNammer: consistent annotation of rRNA genes in genomic sequences. Lagesen K, Hallin PF, Roedland E, Staerfeldt HH, Rognes T Ussery DW. Nucleic Acids Res. Apr 22, 2007. Homepage: http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer Keyword:bio<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://root.cern.ch/drupal/ root/5.34.36]
| align="center" | tools
| align="center" |
| <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: http://root.cern.ch/drupal/ Keyword:tools<br />'''Prerequisites:''' gcc/4.8.5 or gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://root.cern.ch/drupal/ root/6.08.02]
| align="center" | tools
| align="center" |
| <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: http://root.cern.ch/drupal/ Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [https://www.rosettacommons.org rosetta/3.8]
| align="center" | chem
| align="center" |
| <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. Homepage: https://www.rosettacommons.org Keyword:chem<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://deweylab.github.io/RSEM/ rsem/1.3.0]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RNA-Seq by Expectation-Maximization Homepage: http://deweylab.github.io/RSEM/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://www.rstudio.com/ rstudio-server/1.1.206]
| align="center" | tools
| align="center" |
| <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/ Keyword:tools<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://www.rstudio.com/ rstudio-server/1.1.447]
| align="center" | tools
| align="center" |
| <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/ Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://itk.org rtk/1.4.0]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Insighteconstruction Toolkit (RTK) is an open-source and cross-platform software for fast circular cone-beam CT reconstruction based on the Insight Toolkit (ITK). RTK is developped by the RTK consortium. RTK provides or will provide Basic operators for reconstruction, e.g., filtering, forward, projection and backprojection Multithreaded CPU and GPU versions Tools for respiratory motion correction I/O for several scanners Preprocessing of raw data for scatter correction Homepage: https://itk.org Keyword:bio<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://www.ruby-lang.org ruby/2.3.1]
| align="center" | tools
| align="center" |
| <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 Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://rubygems.org rubygems/2.3.1]
| align="center" | tools
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/COMBINE-lab/salmon salmon/0.11.3]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/COMBINE-lab/salmon/ salmonbeta/0.6.0]
| align="center" | bio
| align="center" |
| <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. Salmon achieves is accuracy and speed via a number of different innovations, including the use of quasi-mapping (accurate but fast-to-compute proxies for traditional read alignments), and massively-parallel stochastic collapsed variational inference. The result is a versatile tool that fits nicely into many differnt pipelines. For example, you can choose to make use of our quasi-mapping algorithm by providing Salmon with raw sequencing reads, or, if it is more convenient, you can provide Salmon with regular alignments (e.g. an unsorted BAM file produced with your favorite aligner), and it will use the same wicked-fast, state-of-the-art inference algorithm to estimate transcript-level abundances for your experiment. Homepage: https://github.com/COMBINE-lab/salmon/ Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://lomereiter.github.io/sambamba/ sambamba/0.6.7]
| align="center" | bio
| align="center" |
| <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: http://lomereiter.github.io/sambamba/ Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/GregoryFaust/samblaster samblaster/0.1.24]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.htslib.org/ samtools/0.1.20]
| align="center" | bio
| align="center" |
| <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: http://www.htslib.org/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.htslib.org/ samtools/1.3.1]
| align="center" | bio
| align="center" |
| <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: http://www.htslib.org/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.htslib.org/ samtools/1.5]
| align="center" | bio
| align="center" |
| <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: http://www.htslib.org/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.scala-sbt.org/ sbt/1.1.1]
| align="center" | tools
| align="center" |
| <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/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.netlib.org/scalapack/ scalapack/2.0.2]
| align="center" | math
| align="center" |
| <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: http://www.netlib.org/scalapack/ Keyword:math<br />'''Prerequisites:''' gcc/6.4.0 and cuda/9.0.176 and openmpi/2.1.1 or gcc/6.4.0 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://python.org/ scipy-stack/2017b]
| align="center" | math
| align="center" |
| <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/ Keyword:math<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://python.org/ scipy-stack/2018b]
| align="center" | math
| align="center" |
| <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/ Keyword:math<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://python.org/ scipy-stack/2019a]
| align="center" | math
| align="center" |
| <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/ Keyword:math<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://gforge.inria.fr/projects/scotch/ scotch/6.0.4]
| align="center" | math
| align="center" |
| <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: http://gforge.inria.fr/projects/scotch/ Keyword:math<br />'''Prerequisites:''' gcc/4.8.5 and openmpi/2.1.1 or gcc/5.4.0 and openmpi/2.0.2 or gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2 or intel/2017.1 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://gforge.inria.fr/projects/scotch/ scotch/6.0.6]
| align="center" | math
| align="center" |
| <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: http://gforge.inria.fr/projects/scotch/ Keyword:math<br />'''Prerequisites:''' gcc/7.3.0 and openmpi/3.1.2<br />'''Description:''' </div>
|-
| align="center" | [https://www.disneyanimation.com/technology/seexpr.html seexpr/2.11]
| align="center" | vis
| align="center" |
| <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 />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://www.shengbte.org/ shengbte/1.1.1]
| align="center" | phys
| align="center" |
| <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/ Extensions: thirdorder-1.0.2 Keyword:phys<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1 or intel/2017.1 and openmpi/2.0.2<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/sharpton/shotmap shotmap/1.1]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Shotmap is a software workflow that functionally annotates and compares shotgun metagenomes. Specifically, it will: 1. Compared unassembled or assembled metagenomic sequences to a protein family database 2. Calculate metagenome functional abundance and diversity 3. Compare metagenomes using a variety of statistical and ecological tools 4. Identify protein families that differentiate metagenomes using robust statistical tests Shotmap can be run on a multicore computer or can optionally interface with an SGE-configured computing cluste (i.e., a cloud). Shotmap can also optionally manage the information and data associated with this workflow in a relational database. Homepage: https://github.com/sharpton/shotmap Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://departments.icmab.es/leem/siesta siesta/4.0]
| align="center" | chem
| align="center" |
| <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 Keyword:chem<br />'''Prerequisites:''' gcc/6.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp signalp/4.1f]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive bacteria, Gram-negative bacteria, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. Homepage: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.riverbankcomputing.com/software/sip/ sip/4.19.2]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries. Homepage: http://www.riverbankcomputing.com/software/sip/ Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://www.slicer.org/ slicer/4.10.1]
| align="center" | -
| align="center" |
| <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/<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/google/snappy snappy/1.1.3]
| align="center" | tools
| align="center" |
| <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 Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://sourceforge.net/projects/snpeff/ snpeff/4.3t]
| align="center" | bio
| align="center" |
| <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: http://sourceforge.net/projects/snpeff/ Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://soap.genomics.org.cn/index.html soapdenovo2/r240]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://bioinfo.lifl.fr/RNA/sortmerna/ sortmerna/2.1]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://cab.spbu.ru/software/spades/ spades/3.10.1]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://spark.apache.org spark/2.1.0]
| align="center" | tools
| align="center" | [[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 Keyword:tools CC-Wiki: Apache Spark<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://spark.apache.org spark/2.1.1]
| align="center" | tools
| align="center" | [[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 Keyword:tools CC-Wiki: Apache Spark<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://spark.apache.org spark/2.2.0]
| align="center" | tools
| align="center" | [[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 Keyword:tools CC-Wiki: Apache Spark<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://spark.apache.org spark/2.2.1]
| align="center" | tools
| align="center" | [[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 Keyword:tools CC-Wiki: Apache Spark<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://spark.apache.org spark/2.3.0]
| align="center" | tools
| align="center" | [[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 Keyword:tools CC-Wiki: Apache Spark<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/atztogo/spglib spglib/1.9.9]
| align="center" | chem
| align="center" |
| <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/atztogo/spglib Keyword:chem<br />'''Prerequisites:''' gcc/4.8.5 or gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std sra-toolkit/2.8.2-1]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The NCBI SRA Toolkit enables reading (dumping) of sequencing files from the SRA database and writing (loading) files into the .sra format Homepage: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE-longread sspace-longread/1-1]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/nsoranzo/sspace_basic sspace_basic/2.1.1]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://creskolab.uoregon.edu/stacks/ stacks/1.45]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://catchenlab.life.illinois.edu/stacks/ stacks/1.46]
| align="center" | bio
| align="center" |
| <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://catchenlab.life.illinois.edu/stacks/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://mdx.plm.automation.siemens.com/star-ccm-plus starccm-mixed/11.06.011]
| align="center" | phys
| align="center" | [[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 Keyword:phys CC-Wiki: StarCCM<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://mdx.plm.automation.siemens.com/star-ccm-plus starccm-mixed/12.04.011]
| align="center" | phys
| align="center" | [[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 Keyword:phys CC-Wiki: StarCCM<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://mdx.plm.automation.siemens.com/star-ccm-plus starccm-mixed/12.06.011]
| align="center" | phys
| align="center" | [[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 Keyword:phys CC-Wiki: StarCCM<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://mdx.plm.automation.siemens.com/star-ccm-plus starccm-mixed/13.04.010]
| align="center" | phys
| align="center" | [[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 Keyword:phys CC-Wiki: StarCCM<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://mdx.plm.automation.siemens.com/star-ccm-plus starccm/11.06.011-R8]
| align="center" | phys
| align="center" | [[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 verison uses double precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys CC-Wiki: StarCCM<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://mdx.plm.automation.siemens.com/star-ccm-plus starccm/12.04.011-R8]
| align="center" | phys
| align="center" | [[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 verison uses double precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys CC-Wiki: StarCCM<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://mdx.plm.automation.siemens.com/star-ccm-plus starccm/12.06.011-R8]
| align="center" | phys
| align="center" | [[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 verison uses double precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys CC-Wiki: StarCCM<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://mdx.plm.automation.siemens.com/star-ccm-plus starccm/13.04.010-R8]
| align="center" | phys
| align="center" | [[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 verison uses double precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys CC-Wiki: StarCCM<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://su2.stanford.edu su2/5.0.0]
| align="center" | math
| align="center" |
| <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 Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://su2.stanford.edu su2/6.0.1]
| align="center" | math
| align="center" |
| <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 Keyword:math<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://subread.sourceforge.net/ subread/1.5.2]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://faculty.cse.tamu.edu/davis/suitesparse.html suitesparse/4.5.4]
| align="center" | math
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SuiteSparse is a collection of libraries manipulate sparse matrices. - Homepage: http://faculty.cse.tamu.edu/davis/suitesparse.html Keyword:math<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://metabarcoding.org/sumatra sumaclust/1.0.20]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ superlu/5.1.1]
| align="center" | math
| align="center" |
| <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/ Keyword:math<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome supernova/2.0.0]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome supernova/2.1.1]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://samtools.sourceforge.net tabix/0.2.6]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Generic indexer for TAB-delimited genome position files Homepage: http://samtools.sourceforge.net Keyword:bio<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://software.intel.com/en-us/articles/intel-tbb/ tbb/2017.2.132]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Threading Building Blocks 2017 (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms. Homepage: http://software.intel.com/en-us/articles/intel-tbb/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://01.org/tbb/ tbb/2018_U5]
| align="center" | tools
| align="center" |
| <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://01.org/tbb/ Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.tcl.tk/ tcl/8.5.19]
| align="center" | tools
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm tmhmm/2.0c]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://ccb.jhu.edu/software/tophat/ tophat/2.1.1]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4 or intel/2017.1<br />'''Description:''' </div>
|-
| align="center" | [http://torch.ch/ torch/20170530]
| align="center" | ai
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Torch is a scientific computing framework with wide support for machine learning algorithms that puts GPUs first. It is easy to use and efficient, thanks to an easy and fast scripting language, LuaJIT, and an underlying C/CUDA implementation. Homepage: http://torch.ch/ Keyword:ai<br />'''Prerequisites:''' gcc/5.4.0 and cuda/8.0.44 or intel/2016.4 and cuda/8.0.44<br />'''Description:''' </div>
|-
| align="center" | [http://torch.ch/ torch/20170731]
| align="center" | ai
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Torch is a scientific computing framework with wide support for machine learning algorithms that puts GPUs first. It is easy to use and efficient, thanks to an easy and fast scripting language, LuaJIT, and an underlying C/CUDA implementation. Homepage: http://torch.ch/ Keyword:ai<br />'''Prerequisites:''' intel/2016.4 and cuda/8.0.44<br />'''Description:''' </div>
|-
| align="center" | [http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/ trans-abyss/1.5.5]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [https://transdecoder.github.io/ transdecoder/3.0.1]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://hibberdlab.com/transrate/ transrate/1.0.3]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly. Homepage: http://hibberdlab.com/transrate/ Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://tandem.bu.edu/trf/trf.html trf/4.09]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Tandem repeats finder: a program to analyze DNA sequences. Legacy version. Homepage: https://tandem.bu.edu/trf/trf.html Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://trilinos.sandia.gov/ trilinos/12.10.1]
| align="center" | tools
| align="center" |
| <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: http://trilinos.sandia.gov/ Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://trimal.cgenomics.org/ trimal/1.4]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.usadellab.org/cms/?page=trimmomatic trimmomatic/0.36]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://trinityrnaseq.github.io/ trinity/2.4.0]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0 or intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://trinotate.github.io/ trinotate/3.0.2]
| align="center" | bio
| align="center" |
| <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/ Keyword:bio<br />'''Prerequisites:''' gcc/5.4.0<br />'''Description:''' </div>
|-
| align="center" | [http://www.unidata.ucar.edu/software/udunits/ udunits/2.2.24]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement. Homepage: http://www.unidata.ucar.edu/software/udunits/ Keyword:tools<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://valgrind.org/downloads/ valgrind-mpi/3.13.0]
| align="center" | tools
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Valgrind: Debugging and profiling tools Homepage: http://valgrind.org/downloads/ Keyword:tools<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [https://www.vaultproject.io/ vault/1.0.3]
| align="center" | -
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [https://vcftools.github.io vcftools/0.1.14]
| align="center" | bio
| align="center" |
| <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 Keyword:bio<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://csg.sph.umich.edu/kang/verifyBamID/index.html verifybamid/1.1.3]
| align="center" | bio
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://viennacl.sourceforge.net/ viennacl/1.7.1]
| align="center" | math
| align="center" |
| <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 />'''Prerequisites:''' gcc/5.4.0 and cuda/8.0.44 or intel/2016.4 and cuda/8.0.44<br />'''Description:''' </div>
|-
| align="center" | [http://www.ks.uiuc.edu/Research/vmd vmd/1.9.3]
| align="center" | vis
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Homepage: http://www.ks.uiuc.edu/Research/vmd Keyword:vis<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://math.lbl.gov/voro++/ voro++/0.4.6]
| align="center" | math
| align="center" |
| <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 />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [https://github.com/torognes/vsearch vsearch/2.4.3]
| align="center" | bio
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: VSEARCH stands for vectorized search, as the tool takes advantage of parallelism in the form of SIMD vectorization as well as multiple threads to perform accurate alignments at high speed. VSEARCH uses an optimal global aligner (full dynamic programming Needleman-Wunsch), in contrast to USEARCH which by default uses a heuristic seed and extend aligner. This usually results in more accurate alignments and overall improved sensitivity (recall) with VSEARCH, especially for alignments with gaps. Homepage: https://github.com/torognes/vsearch Keyword:bio<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.vtk.org vtk/6.3.0]
| align="center" | vis
| align="center" |
| <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 Keyword:vis<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
|-
| align="center" | [http://www.vtk.org vtk/8.0.0]
| align="center" | vis
| align="center" |
| <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 Keyword:vis<br />'''Prerequisites:''' gcc/5.4.0 and openmpi/2.1.1 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://software.intel.com/en-us/intel-vtune-amplifier-xe vtune/2018.3]
| align="center" | tools
| align="center" |
| <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: http://software.intel.com/en-us/intel-vtune-amplifier-xe Keyword:tools<br />'''Prerequisites:''' -<br />'''Description:''' </div>
|-
| align="center" | [http://www.wrf-model.org wps/3.8.0]
| align="center" | geo
| align="center" |
| <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 Keyword:geo<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.wrf-model.org wps/3.8.1]
| align="center" | geo
| align="center" |
| <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. Compiled with -DNO_LEAP_CALENDAR Homepage: http://www.wrf-model.org Keyword:geo<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
|-
| align="center" | [http://www.openwfm.org/wiki/WRF-SFIRE wrf-fire/20170625]
| align="center" | geo
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: WRF-Fire combines the Weather Research and Forecasting model (WRF) with a fire code implementing a surface fire behavior model, called SFIRE, based on semi-empirical formulas calculate the rate of spread of the fire line (the interface between burning and unignited fuel) based on fuel properties, wind velocities from WRF, and terrain slope. The fire spread is implemented by the level set method. Homepage: http://www.openwfm.org/wiki/WRF-SFIRE Keyword:geo<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
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| align="center" | [http://www.wrf-model.org wrf/3.8.0]
| align="center" | geo
| align="center" |
| <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: http://www.wrf-model.org Keyword:geo<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
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| align="center" | [http://www.wrf-model.org wrf/3.8.1]
| align="center" | geo
| align="center" |
| <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. Compiled with -DNO_LEAP_CALENDAR Homepage: http://www.wrf-model.org Keyword:geo<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
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| align="center" | [http://www.xcrysden.org/ xcrysden/1.5.60]
| align="center" | vis
| align="center" |
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. Homepage: http://www.xcrysden.org/ Keyword:vis<br />'''Prerequisites:''' intel/2016.4<br />'''Description:''' </div>
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| align="center" | [http://xerces.apache.org/xerces-c/ xerces-c++/3.1.1]
| align="center" | tools
| align="center" |
| <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: http://xerces.apache.org/xerces-c/ Keyword:tools<br />'''Prerequisites:''' - or intel/2016.4<br />'''Description:''' </div>
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| align="center" | [https://www.dkrz.de/redmine/projects/yaxt yaxt/0.5.1]
| align="center" | tools
| align="center" |
| <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 Keyword:tools<br />'''Prerequisites:''' intel/2016.4 and openmpi/2.0.2 or intel/2016.4 and openmpi/2.1.1<br />'''Description:''' </div>
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| align="center" | [http://www.zeromq.org/ zeromq/4.2.5]
| align="center" | tools
| align="center" |
| <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 />'''Prerequisites:''' -<br />'''Description:''' </div>
|}
|}
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