.. _Raxml:

RAxML
=====

De acordo com a `página do Raxml <https://cme.h-its.org/exelixis/web/software/raxml/>`_,
"*Phylogenies are increasingly used in all fields of medical and biological
research. Moreover, because of the next-generation sequencing revolution,
datasets used for conducting phylogenetic analyses grow at an unprecedented
pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for
phylogenetic analyses of large datasets under maximum likelihood. Since the
last RAxML paper in 2006, it has been continuously maintained and extended to
accommodate the increasingly growing input datasets and to serve the needs of
the user community*".


Versões Disponíveis
-------------------

* raxml/8.2.11


Submissão de Jobs em Paralelo
-----------------------------

Crie um arquivo chamado, por exemplo, *submit_paral_jobs.sh*:

.. code-block:: bash

   #!/bin/bash
   #SBATCH -t 24:00:00 -n 8

   export INPUT="raxml-mpi.phy"
   export OUTPUT="*"

   module load raxml
   job-nanny srun -n 8 raxmlHPC-MPI-SSE3 -N 8 -p123 -m PROTGAMMAWAG -s raxml-mpi.phy -n raxml-mpi

Para submeter o processo, basta usar o comando:

.. code-block:: bash

   sbatch submit_paral_jobs.sh

Submissão de Jobs Seriais
-------------------------

Crie um arquivo chamado, por exemplo, *submit_serial_jobs.sh*:

.. code-block:: bash

   #!/bin/bash
   #SBATCH -t 24:00:00 -c 8

   export INPUT="raxml-smp.phy"
   export OUTPUT="*"

   module load raxml
   job-nanny raxmlHPC-PTHREADS-SSE3 -T 8 -p123 -m PROTGAMMAWAG -s raxml-smp.phy -n raxml-smp 

Para submeter o processo, basta usar o comando:

.. code-block:: bash

   sbatch submit_serial_jobs.sh


Referências
-----------

Para informações adicionais sobre o software, consulte a `página do Raxml <https://cme.h-its.org/exelixis/web/software/raxml/>`_.