Difference between revisions of "Beast"
(Created page with "== Introduction == BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict ...") |
Schwietzer (talk | contribs) |
||
| (10 intermediate revisions by 2 users not shown) | |||
| Line 2: | Line 2: | ||
BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies 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 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. | BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies 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 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. | ||
Additionally, since the installed version '''2.6.3''', SNAPP is installed with Beast as well. SNAPP (SNP and AFLP Package for Phylogenetic analysis) is a package for inferring species trees and species demographics from independent (unlinked) biallelic markers such as well spaced SNPs. It implements a full coalescent model, but uses a novel algorithm to integrate over all possible gene trees, rather than sampling them explicitly. [http://www.beast2.org/snapp/ ¹] | |||
== Installed version == | == Installed version == | ||
The currently | The following versions are installed and currently available... <br/> | ||
... on environment ''hpc-env/8.3'': | |||
*'''Beast/2.6.3'''-GCC-8.3.0 | |||
... on environment ''hpc-uniol-env'': | |||
*'''Beast/2.4.5''' | |||
== Using Beast on the Cluster == | == Using Beast on the Cluster == | ||
If you want to use Beast on the cluster, you can do that by loading the corresponding module with the command: | If you want to use Beast on the cluster, you can do that by loading the corresponding module within the right environment with the command: | ||
module load Beast | module load Beast | ||
Afterwards, you can start the Beast GUI by typing in: | |||
beast | |||
Since Beast comes with a grapfical interface, you will have to connect to the server via an X11 port open. You can read more on how to do that on our wiki page about [https://wiki.hpcuser.uni-oldenburg.de/index.php?title=Interactive_Jobs interactive jobs]. | |||
<!-- | |||
== Example == | |||
The following lines of code are an example jobscript for BEAST: | |||
#!/bin/bash | |||
#SBATCH --ntasks=1 | |||
#SBATCH --mem=2G | |||
#SBATCH --time=0-2:00 | |||
#SBATCH --job-name=BCFTOOLS-TEST | |||
#SBATCH --output=beast-test.%j.out | |||
#SBATCH --error=beast-test.%j.err | |||
module load BCFtools/1.3.1-intel-2016b | |||
--> | |||
== Documentation == | == Documentation == | ||
You can find more informations about Beast 2 and even some tutorials | You can find more informations about Beast 2 and even some tutorials on the [http://www.beast2.org/ official website]. | ||
Latest revision as of 18:15, 2 March 2021
Introduction
BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies 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 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability.
Additionally, since the installed version 2.6.3, SNAPP is installed with Beast as well. SNAPP (SNP and AFLP Package for Phylogenetic analysis) is a package for inferring species trees and species demographics from independent (unlinked) biallelic markers such as well spaced SNPs. It implements a full coalescent model, but uses a novel algorithm to integrate over all possible gene trees, rather than sampling them explicitly. ¹
Installed version
The following versions are installed and currently available...
... on environment hpc-env/8.3:
- Beast/2.6.3-GCC-8.3.0
... on environment hpc-uniol-env:
- Beast/2.4.5
Using Beast on the Cluster
If you want to use Beast on the cluster, you can do that by loading the corresponding module within the right environment with the command:
module load Beast
Afterwards, you can start the Beast GUI by typing in:
beast
Since Beast comes with a grapfical interface, you will have to connect to the server via an X11 port open. You can read more on how to do that on our wiki page about interactive jobs.
Documentation
You can find more informations about Beast 2 and even some tutorials on the official website.
