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

Versions

  • 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 -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
ml biocontainers phylofisher