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phylter (version 0.9.12)

Detect and Remove Outliers in Phylogenomics Datasets

Description

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) ), a generalization of classical multidimensional scaling to multiple distance matrices.

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Install

install.packages('phylter')

Monthly Downloads

225

Version

0.9.12

License

GPL (>= 2)

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Maintainer

Aurélie Siberchicot

Last Published

July 29th, 2025

Functions in phylter (0.9.12)

print.summary.phylter

print summary of phylter objects
rename.genes

Name or rename a list of gene trees or matrices
simtrees

Simplistic simulation of gene trees with outliers
print.phylter

Print phylter objects
summary.phylter

Get summary for phylter objects
write.phylter

Write summary of phyter analysis to file(s)
trees2matrices

Convert phylogenetic trees to distance matrices
print.phylterfinal

print objects of class phylterfinal
DistatisFast

Fast implementation the multivariate analysis method Distatis
impMean

Imputation of missing values in a collection of matrices
detect.outliers

Detection of outliers in 1D and 2D data
normalize

Median normalization of 2D matrix by row or by colomn
Dist2WR

Compute gene x species matrix from the result of Distatis
medcouple

A robust measure of skewness for univariate data
plot.phylter

Plot phylter objects
carnivora

125 genes trees for 53 carnivora species
phylter

Filter phylogenomics datasets
PreparePhylterData

Prepare data for phylter analysis
print.phylterinitial

print objects of class phylterinitial