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: 2.3.1
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, seqLogo, seqinr, xtable, flashClust, rgl, knitr, rmarkdown, Biostrings
Published: 2017-11-01
Author: Klaus Schliep [aut, cre], Emmanuel Paradis [aut], Leonardo de Oliveira Martins [aut], Alastair Potts [aut], Tim W. White [aut], Cyrill Stachniss [ctb], Michelle Kendall [ctb]
Maintainer: Klaus Schliep <klaus.schliep at gmail.com>
BugReports: https://github.com/KlausVigo/phangorn/issues
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: https://github.com/KlausVigo/phangorn
NeedsCompilation: yes
Citation: phangorn citation info
Materials: README NEWS
In views: Genetics, Phylogenetics
CRAN checks: phangorn results

Downloads:

Reference manual: phangorn.pdf
Vignettes: Ancestral Sequence Reconstruction
Constructing phylogenetic trees
Advanced features
IntertwiningTreesAndNetworks
Splits and Networx
Package source: phangorn_2.3.1.tar.gz
Windows binaries: r-devel: phangorn_2.3.1.zip, r-release: phangorn_2.3.1.zip, r-oldrel: phangorn_2.3.1.zip
OS X El Capitan binaries: r-release: phangorn_2.3.1.tgz
OS X Mavericks binaries: r-oldrel: phangorn_2.3.1.tgz
Old sources: phangorn archive

Reverse dependencies:

Reverse depends: apex, MonoPhy, phybreak
Reverse imports: BoSSA, coalescentMCMC, CommT, corHMM, genBaRcode, indelmiss, markophylo, OUwie, paleotree, phytools, poppr, RADami, RAM, rdiversity, recluster, rwty, SeqFeatR, strataG, timetree, TKF, TreeSearch, treespace

Linking:

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