Phyx

Introduction

phyx (pronounced ‘fix’) is a collection of Unix-style command-line programs for phylogenetics and sequence/tree manipulation, designed to be composed with pipes inside larger pipelines. Notes There is no single ‘phyx’ executable. The package installs 48 separate ‘px*’ programs, all of which this module puts on the command line. Each takes ‘-h’ for help; see the wiki for a categorised list: https://github.com/FePhyFoFum/phyx/wiki/Program-list Common entry points: pxclsq (clean alignment by occupancy), pxrmk (remove taxa), pxcat (concatenate alignments), pxbp (bipartitions), pxrr (reroot), pxlssq / pxlstr (alignment and tree summary stats). Version note: Bioconda is pinned at 1.1 while upstream is at 1.3.2. Programs added after 1.1 are NOT in this module. Citation: Brown JW, Walker JF, Smith SA. Phyx: phylogenetic tools for unix. Bioinformatics 2017;33(12):1886-1888. doi:10.1093/bioinformatics/btx063

For more information, please check:
BioContainers: https://biocontainers.pro/tools/phyx
Home page: https://github.com/FePhyFoFum/phyx

Note

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

Versions

Cluster

Version(s)

GAUTSCHI

1.1

Commands

  • pxaa2cdn

  • pxbdfit

  • pxbdsim

  • pxboot

  • pxbp

  • pxcat

  • pxclsq

  • pxcltr

  • pxcolt

  • pxcomp

  • pxconsq

  • pxcontrates

  • pxfqfilt

  • pxlog

  • pxlssq

  • pxlstr

  • pxmono

  • pxmrca

  • pxmrcacut

  • pxmrcaname

  • pxnj

  • pxnw

  • pxrecode

  • pxrevcomp

  • pxrls

  • pxrlt

  • pxrmk

  • pxrms

  • pxrmt

  • pxrr

  • pxs2fa

  • pxs2nex

  • pxs2phy

  • pxseqgen

  • pxssort

  • pxsstat

  • pxstrec

  • pxsw

  • pxt2new

  • pxt2nex

  • pxtcol

  • pxtcomb

  • pxtgen

  • pxtlate

  • pxtrt

  • pxtscale

  • pxupgma

  • pxvcf2fa

Module

You can load the modules by:

module load biocontainers
module load phyx

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 phyx 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=phyx
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers phyx

# Your phyx 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=phyx
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers phyx

# Your phyx 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=phyx
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers phyx

# Your phyx 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=phyx
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers phyx

# Your phyx workflow...

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

module --force purge
module biocontainers phyx

# Your phyx workflow...