ASTRAL

Description

astral website  

ASTRAL is a Java program for estimating a species tree given a set of unrooted gene trees. ASTRAL is statistically consistent under multi-species coalescent model (and thus is useful for handling ILS). It finds the tree that maximizes the number of induced quartet trees in the set of gene trees that are shared by the species tree. The algorithm has an exact version that can run for small datasets (less than 18 taxa) and a more useful version that can handle large datasets (103 taxa an 800 genes were analyzed in few minutes).

Environment Modules

Run module spider astral to find out what environment modules are available for this application.

System Variables

• HPC_ASTRAL_DIR - installation directory

Additional Information

To allocate a set amount of memory for ASTRAL (java application), for example 2g run the following command in the terminal or the job script:

export _JAVA_OPTIONS="-Xmx2g"

We provide an 'astral' wrapper script, so java -jar ... doesn't have to be called manually. An example command to run ASTRAL:

$ astral -i simulated_primates_5X.10.gene.tre -o test_out/simulated_primates_5X.10.gene_out.tre

Citation

If you publish research that uses astral you have to cite it as follows:

Mirarab, Siavash, Rezwana Reaz, Md. Shamsuzzoha Bayzid, Theo Zimmermann, M Shel Swenson, and Tandy Warnow. “ASTRAL: Genome-Scale Coalescent-Based Species Tree.” Bioinformatics 30, no. 17 (2014): i541–i548. doi:10.1093/bioinformatics/btu462.