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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