.. _Beast:

Beast
=====

De acordo com a `documentação do Beast <http://beast.community/>`_,
"*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*.

.. code-block:: bash

   #!/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:

.. code-block:: bash

   sbatch submit_jobs.sh


Submissão de jobs com versão Java
---------------------------------

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

.. code-block:: bash

   #!/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 <http://beast.community/>`_.