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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).
Version: | 2.12.1 |
Depends: | ape (≥ 5.8), R (≥ 4.1.0) |
Imports: | digest, fastmatch, generics, graphics, grDevices, igraph (≥ 1.0), Matrix, methods, parallel, quadprog, Rcpp, stats, utils |
LinkingTo: | Rcpp |
Suggests: | apex, Biostrings, ggseqlogo, ggplot2, knitr, magick, rgl, rmarkdown, seqinr, testthat (≥ 3.0.0), tinytest, vdiffr, xtable |
Published: | 2024-09-17 |
DOI: | 10.32614/CRAN.package.phangorn |
Author: | Klaus Schliep [aut, cre], Emmanuel Paradis [aut], Leonardo de Oliveira Martins [aut], Alastair Potts [aut], Iris Bardel-Kahr [aut], 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], Santiago Claramunt [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, https://klausvigo.github.io/phangorn/ |
NeedsCompilation: | yes |
Language: | en-US |
Citation: | phangorn citation info |
Materials: | README NEWS |
In views: | Phylogenetics |
CRAN checks: | phangorn results |
Package source: | phangorn_2.12.1.tar.gz |
Windows binaries: | r-devel: phangorn_2.12.1.zip, r-release: phangorn_2.12.1.zip, r-oldrel: phangorn_2.12.1.zip |
macOS binaries: | r-release (arm64): phangorn_2.12.1.tgz, r-oldrel (arm64): phangorn_2.12.1.tgz, r-release (x86_64): phangorn_2.12.1.tgz, r-oldrel (x86_64): phangorn_2.12.1.tgz |
Old sources: | phangorn archive |
Reverse depends: | apex, MSCquartets, windex |
Reverse imports: | babette, beastier, BoSSA, BSS, coalescentMCMC, corHMM, DCLEAR, dispRity, dowser, EnvNJ, genBaRcode, haplotypes, hisse, immunarch, indelmiss, ips, LDM, LymphoSeq, markophylo, MesKit, microbial, MonoPhy, nodeSub, orthGS, OUwie, paleotree, pcmabc, philr, phyloregion, phytools, POMS, ppgm, rapidphylo, recluster, RPANDA, rwty, scistreer, SeqFeatR, sketching, STraTUS, tanggle, TML, treespace |
Reverse suggests: | ape, compcodeR, CongreveLamsdell2016, gromovlab, mcbette, MicrobiotaProcess, MiscMetabar, msa, Platypus, Quartet, RevGadgets, RRphylo, shipunov, tracerer, TreeDist, treeio, TreeSearch, TreeTools |
Reverse enhances: | dendextend |
Please use the canonical form https://CRAN.R-project.org/package=phangorn to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.