recipe treesimulator

Simulation of rooted phylogenetic trees under a given Multitype Birth–Death (MTBD) model.

Homepage:

https://github.com/evolbioinfo/treesimulator

License:

GPL3 / GPL-3.0-or-later

Recipe:

/treesimulator/meta.yaml

Treesimulator provides fast methods for simulation of rooted phylogenetic trees under Multitype Birth–Death (MTBD) models, in particular the classical BD model, the BD Exposed-Infectious (BDEI) model, and BD with superspreading (BDSS).

package treesimulator

(downloads) docker_treesimulator

versions:

0.2.0-0,  0.1.22-0

depends ete3:

>=3.1.1

depends numpy:

>=1.22

depends python:

>=3.9

depends scipy:

>=1.5.0

depends six:

>=1.16.0

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 treesimulator

and update with::

   mamba update treesimulator

To create a new environment, run:

mamba create --name myenvname treesimulator

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/treesimulator:<tag>

(see `treesimulator/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/treesimulator/README.html)