recipe bioconductor-tanggle

Visualization of Phylogenetic Networks

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/tanggle.html

License:

Artistic-2.0

Recipe:

/bioconductor-tanggle/meta.yaml

Offers functions for plotting split (or implicit) networks (unrooted, undirected) and explicit networks (rooted, directed) with reticulations extending. 'ggtree' and using functions from 'ape' and 'phangorn'. It extends the 'ggtree' package [@Yu2017] to allow the visualization of phylogenetic networks using the 'ggplot2' syntax. It offers an alternative to the plot functions already available in 'ape' Paradis and Schliep (2019) <doi:10.1093/bioinformatics/bty633> and 'phangorn' Schliep (2011) <doi:10.1093/bioinformatics/btq706>.

package bioconductor-tanggle

(downloads) docker_bioconductor-tanggle

versions:

1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.0.0-0

depends bioconductor-ggtree:

>=3.14.0,<3.15.0

depends r-ape:

>=5.0

depends r-base:

>=4.4,<4.5.0a0

depends r-ggplot2:

>=2.2.0

depends r-phangorn:

>=2.5

requirements:

additional platforms:

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 bioconductor-tanggle

and update with::

   mamba update bioconductor-tanggle

To create a new environment, run:

mamba create --name myenvname bioconductor-tanggle

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/bioconductor-tanggle:<tag>

(see `bioconductor-tanggle/tags`_ for valid values for ``<tag>``)

Download stats

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/bioconductor-tanggle/README.html)