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). Note: export _JAVA_OPTIONS="-Xmx?g" where ? equals to the available memory.

Environment Modules

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

Environment Variables

• HPC_ASTRAL_DIR - installation directory
• HPC_ASTRAL_BIN - executable directory
• HPC_ASTRAL_DOC - documentation directory
• HPC_ASTRAL_TEST - test data directory

Additional Usage 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 simulated_primates_5X.10.gene_out.tre

Categories

biology, ngs, phylogenetics