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).

Package overview README.md Ancestral Sequence Reconstruction Estimating phylogenetic trees with phangorn Intertwining phylogenetic trees and networks: R Example Script Markov models and transition rate matrices Maximum likelihood by hand Phylogenetic trees from morphological data Splits and Networx

Vignettes Man pages API and functions Files

Package details
Author	Klaus Schliep [aut, cre] (<https://orcid.org/0000-0003-2941-0161>), Emmanuel Paradis [aut] (<https://orcid.org/0000-0003-3092-2199>), Leonardo de Oliveira Martins [aut] (<https://orcid.org/0000-0001-5247-1320>), Alastair Potts [aut], Iris Bardel-Kahr [aut] (<https://orcid.org/0000-0002-8950-834X>), Tim W. White [ctb], Cyrill Stachniss [ctb], Michelle Kendall [ctb], Keren Halabi [ctb], Richel Bilderbeek [ctb], Kristin Winchell [ctb], Liam Revell [ctb], Mike Gilchrist [ctb], Jeremy Beaulieu [ctb], Brian O'Meara [ctb], Long Qu [ctb], Joseph Brown [ctb] (<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [ctb] (<https://orcid.org/0000-0002-8926-5974>)
Bioconductor views	QualityControl Software Technology
Maintainer	Klaus Schliep <klaus.schliep@gmail.com>
License	GPL (>= 2)
Version	2.12.1
URL	https://github.com/KlausVigo/phangorn https://klausvigo.github.io/phangorn/
Package repository	View on CRAN
Installation	Install the latest version of this package by entering the following in R: `install.packages("phangorn")`