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-appsmodule.
Usage
PHYLIP is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the PHYLIP module:
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:
The programs are interactive by default. For batch use, provide the responses via a response file, for example:
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.