PHYLIP

PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). It includes methods such as parsimony, distance matrix and maximum likelihood, and tools for consensus trees, bootstrapping and tree drawing.

• PHYLIP
  • License
  • Available
  • Usage
    • Example batch script
  • Support
  • More information

License

Free to use. See the PHYLIP home page for license terms.

Available

• Roihu: 3.697, via the bio-apps module.

Usage

PHYLIP is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the PHYLIP module:

module load bio-apps/v202603
module load phylip/3.697

PHYLIP consists of many individual programs (for example dnaml, dnapars, neighbor, consense). Each program reads a file named infile from the working directory (or prompts for the input file name) and is run by its name:

dnaml

The programs are interactive by default. For batch use, provide the responses via a response file, for example:

dnaml < responses.txt

Example batch script

#!/bin/bash
#SBATCH --job-name=phylip
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=02:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=2G

module load bio-apps/v202603
module load phylip/3.697

dnaml < responses.txt

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information

• PHYLIP home page

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