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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

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.

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

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