rename.genes

Name or rename a list of gene trees or gene matrices genes. For internal use mostly.

Analyzis and filtering of phylogenomics datasets.
It takes an input either a collection of gene trees (then transformed to matrices) or directly a collection of gene matrices and performs an iterative process to identify
what species in what genes are outliers, and whose elimination significantly improves the concordance between the input matrices. The methods builds upon the Distatis approach (Abdi et al. (2005) <doi:10.1101/2021.09.08.459421>), a generalization of classical multidimensional scaling to multiple distance matrices.

Aurélie Siberchicot

phylter

Detect and Remove Outliers in Phylogenomics Datasets

Damien M. de Vienne

Stéphane Dray

Théo Tricou

rename.genes function

<dl><dt>X</dt>
<dd>A list of trees or matrices</dd>
<dt>gene.names</dt>
<dd>List of names to assign to the elements of X. Must be of the same length as length(X). 
If NULL (the default) the object are numbered 1,2,...,length(X).</dd></dl>

Arguments

Name or rename a list of gene trees or matrices — rename.genes

<dl>

<dt>X</dt>
<dd>A list of trees or matrices</dd>


<dt>gene.names</dt>
<dd>List of names to assign to the elements of X. Must be of the same length as length(X). 
If NULL (the default) the object are numbered 1,2,...,length(X).</dd>

</dl>

rename.genes: Name or rename a list of gene trees or matrices

Description

Usage

Value

Arguments

Examples