phangorn: Phylogenetic Analysis in R

Phylogenetic analysis in R: Estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation.

Version: 1.99.14
Depends: R (≥ 3.0.0), ape (≥ 3.3)
Imports: quadprog, igraph (≥ 0.6), Matrix, parallel, nnls, methods, utils, stats, graphics, grDevices
Suggests: testthat, seqLogo, seqinr, xtable, flashClust, rgl, knitr
Published: 2015-07-09
Author: Klaus Schliep, Emmanuel Paradis
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_1.99.14.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
OS X Snow Leopard binaries: r-release: phangorn_1.99.14.tgz, r-oldrel: phangorn_1.99-7.tgz
OS X Mavericks binaries: r-release: phangorn_1.99.14.tgz
Old sources: phangorn archive

Reverse dependencies:

Reverse depends: apex, MonoPhy
Reverse imports: coalescentMCMC, CommT, corHMM, markophylo, OUwie, paleotree, phytools, poppr, RADami, RAM, recluster, SeqFeatR, timetree, TKF, treescape