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.

• ASTRAL
  • License
  • Available
  • Usage
  • Support
  • More information

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

• ASTRAL GitHub repository

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