phangorn
Phylogenetic Reconstruction and Analysis
Allows for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation (Schliep 2011). Offers methods for tree comparison, model selection and visualization of phylogenetic networks as described in Schliep et al. (2017).
phangorn 
phangorn is a package for phylogenetic reconstruction and analysis in the R language. phangorn offers the possibility of reconstructing phylogenies with distance based methods, maximum parsimony or maximum likelihood (ML) and performing Hadamard conjugation. Extending the general ML framework, this package provides the possibility of estimating mixture and partition models. Furthermore, phangorn offers several functions for comparing trees, phylogenetic models or splits, simulating character data and performing congruence analyses.
To get an introduction into phylogenetic inference you want to look at:
vignette("Trees", package="phangorn")
Installation
You can install the the latest release phangorn of the package from
CRAN, or the development version
from github or
r-universe.
| Type | Source | Command |
|---|---|---|
| Release | CRAN | install.packages("phangorn") |
| Development | GitHub | remotes::install_github("KlausVigo/phangorn") |
| Development | r-universe | install.packages('phangorn', repos = 'https://klausvigo.r-universe.dev') |
To install the development version you may need to install the Biostrings package from bioconductor first:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Biostrings")
To use all functionality you might install all you might need to install the
rgl and ggseqlogo package.
install.packages("rgl")
install.packages("ggseqlogo")
The development version usually depends on the latest ape development
version and information to download can be found
here.
Citation
If you use phangorn please cite:
Schliep K.P. 2011. phangorn: phylogenetic analysis in R. Bioinformatics, 27(4) 592-593
License
phangorn is licensed under the GPLv2.