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phylter
View on CRAN: Click
here
Download and install phylter package within the R console
Install from CRAN:
install.packages("phylter")
Install from Github:
library("remotes")
install_github("cran/phylter")
Install by package version:
library("remotes")
install_version("phylter", "0.9.11")
Attach the package and use:
library("phylter")
Maintained by
Aurélie Siberchicot
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2023-01-20
Latest Update: 2023-08-24
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.
How to cite:
Aurélie Siberchicot (2023). phylter: Detect and Remove Outliers in Phylogenomics Datasets. R package version 0.9.11, https://cran.r-project.org/web/packages/phylter. Accessed 07 Nov. 2024.
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imports, suggests or enhances
Complete documentation for phylter
Functions, R codes and Examples using
the phylter R package
Some associated functions: Dist2WR . DistatisFast . PreparePhylterData . carnivora . detect.outliers . impMean . medcouple . normalize . phylter . plot.phylter . print.phylter . print.phylterfinal . print.phylterinitial . print.summary.phylter . rename.genes . simtrees . summary.phylter . trees2matrices . write.phylter .
Some associated R codes: Dist2WR.R . DistatisFast.R . PreparePhylterData.R . data.R . detect.outliers.R . impMean.R . medcouple.R . normalize.R . phylter.R . plot.phylter.R . rename.genes.R . simtrees.R . summary.phylter.R . trees2matrices.R . write.phylter.R . Full phylter package functions and examples
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