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

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:

#!/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...

#!/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...

#!/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...

#!/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...

#!/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...