.. _backbone-label:

Phylofisher
==============================

Introduction
~~~~~~~~
PhyloFisher is a software package written in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of eukaryotic protein sequences.


| For more information, please check:
| Home page: https://github.com/TheBrownLab/PhyloFisher

.. note::
    Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions
~~~~~~~
.. list-table::
  :width: 100 %
  :widths: 25 75
  :header-rows: 1

  * - Cluster
    - Version(s)

  * - ANVIL
    - 1.2.7, 1.2.9
  * - BELL
    - 1.2.7, 1.2.9
  * - GAUTSCHI
    - 1.2.7, 1.2.9
  * - NEGISHI
    - 1.2.7, 1.2.9
  * - SCHOLAR
    - 1.2.7, 1.2.9

Commands
~~~~~~~
- aa_comp_calculator.py
- aa_recoder.py
- apply_to_db.py
- astral_runner.py
- backup_restoration.py
- bipartition_examiner.py
- build_database.py
- config.py
- edirect.py
- explore_database.py
- fast_site_remover.py
- fast_taxa_remover.py
- fisher.py
- forest.py
- genetic_code_examiner.py
- gfmix_runner.py
- heterotachy.py
- informant.py
- install_deps.py
- jp.py
- mammal_modeler.py
- matrix_constructor.py
- prep_final_dataset.py
- purge.py
- random_resampler.py
- rst2html.py
- rst2html4.py
- rst2html5.py
- rst2latex.py
- rst2man.py
- rst2odt.py
- rst2odt_prepstyles.py
- rst2pseudoxml.py
- rst2s5.py
- rst2xetex.py
- rst2xml.py
- rstpep2html.py
- rtc_binner.py
- runxlrd.py
- select_orthologs.py
- select_taxa.py
- sgt_constructor.py
- taxon_collapser.py
- vba_extract.py
- windowmasker_2.2.22_adapter.py
- working_dataset_constructor.py

Module
~~~~~~~~
You can load the modules by::

    module load biocontainers
    module load phylofisher

Example job
~~~~~
.. warning::
    Using ``#!/bin/sh -l`` as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use ``#!/bin/bash`` instead.

To run phylofisher on our clusters:

.. tab-set::

  .. tab-item:: Anvil

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A myallocation     # Allocation name
        #SBATCH -p wholenode        # Partition name
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=phylofisher
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers phylofisher

        # Your phylofisher workflow...

  .. tab-item:: Bell, Gautschi, or Negishi

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A mygroup     # Group name
        #SBATCH -p cpu         # Partition name
        #SBATCH -q normal      # QOS name (optional)
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=phylofisher
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers phylofisher

        # Your phylofisher workflow...

  .. tab-item:: Gautschi-AI

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A mygroup     # Group name
        #SBATCH -p ai          # Partition name
        #SBATCH --gres=gpu:1   # Number of GPUs
        #SBATCH -q normal      # QOS name (optional)
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=phylofisher
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers phylofisher

        # Your phylofisher workflow...

  .. tab-item:: Gilbreth

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A mygroup     # Group name
        #SBATCH -p a100        # Partition name
        #SBATCH --gres=gpu:1   # Number of GPUs
        #SBATCH --mem=2G       # Memory
        #SBATCH -q normal      # QOS name (optional)
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=phylofisher
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers phylofisher

        # Your phylofisher workflow...

  .. tab-item:: Scholar

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A queue     # Queue name
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=phylofisher
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers phylofisher

        # Your phylofisher workflow...