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).

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年09月17日
DOI: 10.32614/CRAN.package.phangorn
Author: Klaus Schliep ORCID iD [aut, cre], Emmanuel Paradis ORCID iD [aut], Leonardo de Oliveira Martins ORCID iD [aut], Alastair Potts [aut], Iris Bardel-Kahr ORCID iD [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 ORCID iD [ctb], Santiago Claramunt ORCID iD [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

Documentation:

Reference manual: phangorn.html , phangorn.pdf
Vignettes: Markov models and transition rate matrices (source, R code)
Ancestral Sequence Reconstruction (source, R code)
Intertwining phylogenetic trees and networks: R Example Script (source, R code)
Maximum likelihood by hand (source, R code)
Phylogenetic trees from morphological data (source, R code)
Splits and Networx (source, R code)
Estimating phylogenetic trees with phangorn (source, R code)

Downloads:

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 dependencies:

Reverse depends: apex, MSCquartets, windex
Reverse imports: babette, beastier, bioregion, BoSSA, BSS, coalescentMCMC, corHMM, DCLEAR, dispRity, dowser, DspikeIn, EnvNJ, EvoPhylo, genBaRcode, haplotypes, hisse, indelmiss, LDM, LymphoSeq, markophylo, MesKit, microbial, MonoPhy, nodeSub, orthGS, OUwie, paleotree, pcmabc, philr, phyloregion, phytools, POMS, ppgm, rapidphylo, recluster, rwty, scistreer, SeqFeatR, sketching, STraTUS, tanggle, taxize, TML, treespace
Reverse suggests: AntibodyForests, ape, compcodeR, CongreveLamsdell2016, gromovlab, immunarch, mcbette, MicrobiotaProcess, MiscMetabar, msa, Platypus, Quartet, RevGadgets, RRphylo, tracerer, TreeDist, treeio, TreeSearch, treestructure, TreeTools
Reverse enhances: dendextend

Linking:

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