trees2matrices

Transform a list of phylogenetic trees into a 
list of phylogenetic distance matrices.

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

trees2matrices function

<dl><dt>trees</dt>
<dd>A list of gene trees in format "multiphylo".</dd>
<dt>distance</dt>
<dd>A method to generate distance matrices. It could be "nodal"
to establish that the distance between two species is the number of nodes
that separate them. Or "patristic" (default) if the distance between two
species is the sum of branch lengths separating them. The "nodal" option should
only be used if all species are present in all trees (no missing data).</dd>
<dt>bvalue</dt>
<dd>This argument is only used if trees contain bootstrap values.
It determines under what bootstrap values the nodes should be collapsed.
Value 0 (the default) means that no nodes are collapsed.</dd></dl>

Arguments

Convert phylogenetic trees to distance matrices — trees2matrices

<dl>

<dt>trees</dt>
<dd>A list of gene trees in format "multiphylo".</dd>


<dt>distance</dt>
<dd>A method to generate distance matrices. It could be "nodal"
to establish that the distance between two species is the number of nodes
that separate them. Or "patristic" (default) if the distance between two
species is the sum of branch lengths separating them. The "nodal" option should
only be used if all species are present in all trees (no missing data).</dd>


<dt>bvalue</dt>
<dd>This argument is only used if trees contain bootstrap values.
It determines under what bootstrap values the nodes should be collapsed.
Value 0 (the default) means that no nodes are collapsed.</dd>

</dl>

trees2matrices: Convert phylogenetic trees to distance matrices

Description

Usage

Value

Arguments

Examples