Learn R Programming

MonoPhy (version 1.3.2)

Explore Monophyly of Taxonomic Groups in a Phylogeny

Description

Requires rooted phylogeny as input and creates a table of genera, their monophyly-status, which taxa cause problems in monophyly etc. Different information can be extracted from the output and a plot function allows visualization of the results in a number of ways. "MonoPhy: a simple R package to find and visualize monophyly issues." Schwery, O. & O'Meara, B.C. (2016) .

Copy Link

Version

Install

install.packages('MonoPhy')

Monthly Downloads

190

Version

1.3.2

License

GPL-3

Maintainer

Orlando Schwery

Last Published

October 17th, 2024

Functions in MonoPhy (1.3.2)

MonoPhy-package

Explore Monophyly of Taxonomic Groups in a Phylogeny.

CollapseMonophyletics

Get tree with collapsed monophyletic groups

Get MRCA nodes of taxonomic groups from 'AssessMonophyly' output

GetResultMonophyly

Get main result table from 'AssessMonophyly' output

GetIntruderTaxa

Get taxa or tips which are intruders or outliers to a taxon from AssessMonophyly

Plot output of AssessMonophyly

AssessMonophyly

Assesses monophyly (or lack of it) of taxonomic groups in a phylogeny.

Example dataset for the package MonoPhy.