.. _PFinderUCE-SWSC-EN:

PFinderUCE-SWSC-EN
==================

De acordo com a `página do PFinderUCE-SWSC-EN <https://github.com/Tagliacollo/PFinderUCE-SWSC-EN>`_,
"*Entropy-based automatic partitioning of UCE alignments: The accuracy of phylogenetic
inferences often depends on choosing an appropriate model of molecular evolution.
In Tagliacollo & Lanfear (submitted), we evaluated the performance of two new
partitioning methods for phylogenomics studies of UCES, and conclude that automatic
selection of partitions through the SWSC-EN method considerably improves model-fit
and parameter estimates. This repository contains scripts to run the SWSC-EN method
on your own alignments. For more information about the method, please see the
accompanying paper, and the repository for replicating the analyses in that paper.
In brief, this method uses entropy to attempt to split each UCE into 3 parts - a
middle part (which is usually quite conserved), and two flanking regions (which
are typically more variable). This parts can then be used as input to e.g.
PartitionFinder2, which can optimise the partitioning scheme by joining together
similar subsets (e.g. it is often the case that a lot of the central regions are
better analysed together than separately).*"


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

* pfinderuce-swsc-en/1.0.0


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

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

.. code-block:: bash

   #!/bin/bash
   #SBATCH -t 23:00:00

   module load pfinderuce-swsc-en/1.0.0

   ln -s $PFinderUCE_SWSC_EN/SWSCEN.py            SWSCEN.py
   ln -s $PFinderUCE_SWSC_EN/utilities.py         utilities.py
   ln -s $PFinderUCE_SWSC_EN/functions_metrics.py functions_metrics.py

   export WORK_DIR=$PWD

   export INPUT="$WORK_DIR/example_dataset.nex"
   export OUTPUT="*"

   job-nanny python SWSCEN.py $WORK_DIR/example_dataset.nex

.. important::
   Dois pontos a serem observados na criação do script de submissão:
   
     * é necessária a criação dos links simbólicos para localizar os scripts em ``python``;
     * é necessário informar o caminho completo para o arquivo de input (*.nex*);
     * a variável ``WORK_DIR`` é padrão e deve ser mantida.

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 PFinderUCE-SWSC-EN <https://github.com/Tagliacollo/PFinderUCE-SWSC-EN>`_.