Difference between revisions of "ASTRAL"
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
|||
| (One intermediate revision by the same user not shown) | |||
| Line 1: | Line 1: | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]][[Category:NGS]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|astral}} | |{{#vardefine:app|astral}} | ||
| Line 20: | Line 20: | ||
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). | 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). | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | |||
| − | < | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{uc:{{#var:app}}}}_DIR | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
| Line 73: | Line 63: | ||
<!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | <!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | ||
__NOTOC____NOEDITSECTION__ | __NOTOC____NOEDITSECTION__ | ||
| − | |||
| − | |||
Latest revision as of 15:08, 12 August 2022
Description
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.