phangorn: Phylogenetic Reconstruction and Analysis

Package contains methods for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks.

Version: 2.5.5
Depends: R (≥ 3.2.0), ape (≥ 5.0)
Imports: quadprog, igraph (≥ 1.0), Matrix, parallel, methods, utils, stats, graphics, grDevices, fastmatch, magrittr, Rcpp (≥ 0.12.0)
LinkingTo: Rcpp
Suggests: testthat, vdiffr, seqinr, xtable, rgl, knitr, rmarkdown, Biostrings
Published: 2019-06-19
Author: Klaus Schliep ORCID iD [aut, cre], Emmanuel Paradis ORCID iD [aut], Leonardo de Oliveira Martins ORCID iD [aut], Alastair Potts [aut], Tim W. White [aut], Cyrill Stachniss [ctb], Michelle Kendall [ctb], Keren Halabi [ctb], Richel Bilderbeek [ctb], Kristin Winchell [ctb]
Maintainer: Klaus Schliep <klaus.schliep at>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
Citation: phangorn citation info
Materials: README NEWS
In views: Genetics, Phylogenetics
CRAN checks: phangorn results


Reference manual: phangorn.pdf
Vignettes: Ancestral Sequence Reconstruction
Constructing phylogenetic trees
Advanced features
Splits and Networx
Package source: phangorn_2.5.5.tar.gz
Windows binaries: r-devel:, r-devel-gcc8:, r-release:, r-oldrel:
OS X binaries: r-release: phangorn_2.5.5.tgz, r-oldrel: phangorn_2.5.5.tgz
Old sources: phangorn archive

Reverse dependencies:

Reverse depends: apex, MonoPhy, MSCquartets, phybreak
Reverse imports: babette, beastier, BoSSA, coalescentMCMC, CommT, corHMM, dispRity, genBaRcode, haplotypes, indelmiss, ips, liayson, LymphoSeq, markophylo, OUwie, paleotree, pcmabc, philr, phytools, poppr, prewas, RAM, rdiversity, recluster, RRphylo, rwty, selac, SeqFeatR, strataG, STraTUS, taxize, timetree, TKF, TreeSearch, treespace, TreeTools
Reverse suggests: CongreveLamsdell2016, msa, Quartet, shipunov, tracerer, treeio


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