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 openjdk:

>=11

depends python:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install astral-tree

and update with::

   mamba update astral-tree

To create a new environment, run:

mamba create --name myenvname astral-tree

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, 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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