recipe astral-tree

ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees.

Homepage:

https://github.com/smirarab/ASTRAL

License:

APACHE / Apache License 2.0

Recipe:

/astral-tree/meta.yaml

Links:

doi: 10.1186/s12859-018-2129-y

ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees. ASTRAL is statistically consistent under the multi-species coalescent model (and thus is useful for handling incomplete lineage sorting, i.e., ILS). ASTRAL finds the species tree that has the maximum number of shared induced quartet trees with the set of gene trees, subject to the constraint that the set of bipartitions in the species tree comes from a predefined set of bipartitions. This predefined set is empirically decided by ASTRAL (but see tutorial on how to expand it). The current code corresponds to ASTRAL-III.

package astral-tree

(downloads) docker_astral-tree

Versions:

5.7.8-0

Depends:
Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install astral-tree

and update with:

conda update astral-tree

or use the docker container:

docker pull quay.io/biocontainers/astral-tree:<tag>

(see astral-tree/tags for valid values for <tag>)

Notes

astral is a Java program that comes with a custom wrapper shell script. By default 'no default java option' is set in the wrapper. The command that runs the program is 'astral'. If you want to overwrite it you can specify memory options directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with 'biopet-fastqsplitter -Xms512m -Xmx1g'.

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