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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.

ASTRAL

ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees. It is statistically consistent under the multi-species coalescent model and is suitable for species-tree estimation in the presence of incomplete lineage sorting.

License

Free to use and open source under the Apache 2.0 license.

Available

  • Roihu: 5.7.1, via the bio-apps module.

Usage

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

module load bio-apps/v202603
module load astral/5.7.1

ASTRAL takes a file of gene trees (one Newick tree per line) as input and writes the estimated species tree. Run it with the astral command:

astral -i gene_trees.tre -o species_tree.tre

The module sets the ASTRAL_HOME environment variable, pointing to the installation (which contains the jar file and the lib directory).

For larger datasets, run ASTRAL as a batch job:

#!/bin/bash
#SBATCH --job-name=astral
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=04:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=8G

module load bio-apps/v202603
module load astral/5.7.1

astral -i gene_trees.tre -o species_tree.tre

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