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Bioconductor - tanggle (development version)

tanggle

This is the development version of tanggle; for the stable release version, see tanggle.

Visualization of Phylogenetic Networks

Bioconductor version: Development (3.22)

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) and 'phangorn' Schliep (2011) .

Author: Klaus Schliep [aut, cre] ORCID: 0000-0003-2941-0161 , Marta Vidal-Garcia [aut], Claudia Solis-Lemus [aut] ORCID: 0000-0002-9789-8915 , Leann Biancani [aut], Eren Ada [aut], L. Francisco Henao Diaz [aut], Guangchuang Yu [ctb], Joshua Justison [aut]

Maintainer: Klaus Schliep <klaus.schliep at gmail.com>

Citation (from within R, enter citation("tanggle")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("tanggle")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("tanggle")
***tanggle***: Visualización de redes filogenéticas con *ggplot2* HTML R Script ***tanggle***: Visualization of phylogenetic networks in a *ggplot2* framework HTML R Script Reference Manual PDF NEWS Text Details biocViews Alignment, Clustering, DataImport, MultipleSequenceAlignment, Phylogenetics, Software, Visualization Version 1.15.2 In Bioconductor since BioC 3.14 (R-4.1) (3.5 years) License Artistic-2.0 Depends R (>= 4.1), ggplot2 (>= 2.2.0), ggtree Imports ape (>= 5.0), phangorn (>= 2.12), utils, methods System Requirements URL https://klausvigo.github.io/tanggle https://github.com/KlausVigo/tanggle Bug Reports https://github.com/KlausVigo/tanggle/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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