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BEAST: Difference between revisions
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== Description == | == Description == <!--T:1--> | ||
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BEAST<ref name="homepage">BEAST2 Homepage: http://beast2.org/</ref> 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. | BEAST<ref name="homepage">BEAST2 Homepage: http://beast2.org/</ref> 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. | ||
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BEAST can use the beagle-lib<ref>Beagle-lib Homepage: https://github.com/beagle-dev/beagle-lib</ref>, which is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. | BEAST can use the beagle-lib<ref>Beagle-lib Homepage: https://github.com/beagle-dev/beagle-lib</ref>, which is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. | ||
== Usage == | == Usage == <!--T:4--> | ||
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Loading the BEAST module with: <code>module load beast</code>, will automatically load it's dependencies, namely the <code>beagle-lib</code> and <code>java</code> modules, and set the environment variable <code>EBROOTBEAST</code> to point to the directory where BEAST's program files are located. | Loading the BEAST module with: <code>module load beast</code>, will automatically load it's dependencies, namely the <code>beagle-lib</code> and <code>java</code> modules, and set the environment variable <code>EBROOTBEAST</code> to point to the directory where BEAST's program files are located. | ||
=== Managing BEAST Packages/Add-ons === | === Managing BEAST Packages/Add-ons === <!--T:6--> | ||
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BEAST has been installed without any add-ons. You can use the <code>addonmanager</code>-command to install the desired add-ons within your home-directory. | BEAST has been installed without any add-ons. You can use the <code>addonmanager</code>-command to install the desired add-ons within your home-directory. | ||
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For more information on how to manage BEAST packages please read | For more information on how to manage BEAST packages please read | ||
the section "Server machines" at: http://www.beast2.org/managing-packages/ | the section "Server machines" at: http://www.beast2.org/managing-packages/ | ||
=== Simple Jobscript for BEAST === | === Simple Jobscript for BEAST === <!--T:9--> | ||
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=== Jobscript for BEAST with more Memory === | === Jobscript for BEAST with more Memory === <!--T:10--> | ||
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== References == | == References == <!--T:11--> | ||
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