Beast

De acordo com a documentação do Beast, “BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. 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. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.”

Versões disponíveis

beast/1.10.4
beast/1.8.4
beast/2.4.7 (default)

Submissão de jobs com memória compartilhada

Crie um arquivo chamado, por exemplo, submit_jobs.sh.

#!/bin/bash
#SBATCH -t 5-00 -c 56

export INPUT="input.xml"
export OUTPUT="*.log *.ops *.trees"

module load beast/1.10.4
job-nanny beast -beagle_instances 56 -threads 56 -beagle_multipartition on P4_2.xml

Para submeter o processo, basta usar o comando:

sbatch submit_jobs.sh

Submissão de jobs com versão Java

Crie um arquivo chamado, por exemplo, submit_jobs.sh.

#!/bin/bash
#SBATCH -t 5-00 -c 8

export INPUT="input.xml"
export OUTPUT="*.log *.ops *.trees"

module load beast/2.4.7
job-nanny java -jar $BEAST_DIR/lib/beast.jar input.xml

A variável de ambiente BEAST_DIR contém o caminho onde o Beast está instalado.

Referência

Para informações adicionais sobre o software, consulte a documentação do Beast.