Allows for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. Offers methods for tree comparison, model selection and visualization of phylogenetic networks as described in Schliep et al. (2017) <doi:10.1111/2041-210X.12760>.
| Version: | 2.6.3 |
| Depends: | ape (≥ 5.4), R (≥ 3.6.0) |
| Imports: | fastmatch, graphics, grDevices, igraph (≥ 1.0), magrittr, Matrix, methods, parallel, quadprog, Rcpp (≥ 1.0.4), stats, utils |
| LinkingTo: | Rcpp |
| Suggests: | Biostrings, knitr, magick, prettydoc, rgl, rmarkdown, seqinr, seqLogo, tinytest, xtable |
| Published: | 2021-04-06 |
| 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],
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] |
| 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 |
| Reference manual: | phangorn.pdf |
| Vignettes: |
Advanced features Ancestral Sequence Reconstruction Intertwining phylogenetic trees and networks: R Example Script Splits and Networx Estimating phylogenetic trees with phangorn |
| Package source: | phangorn_2.6.3.tar.gz |
| Windows binaries: | r-devel: phangorn_2.6.2.zip, r-release: phangorn_2.6.2.zip, r-oldrel: phangorn_2.6.3.zip |
| macOS binaries: | r-release: phangorn_2.6.3.tgz, r-oldrel: phangorn_2.6.3.tgz |
| Old sources: | phangorn archive |
| Reverse depends: | apex, MonoPhy, MSCquartets, sangeranalyseR, windex |
| Reverse imports: | babette, beastier, BoSSA, BSS, coalescentMCMC, CommT, corHMM, dispRity, genBaRcode, haplotypes, indelmiss, ips, liayson, LymphoSeq, markophylo, MesKit, microbial, OUwie, paleotree, pcmabc, philr, phyloregion, phytools, prewas, RAM, recluster, rwty, selac, SeqFeatR, STraTUS, taxize, timetree, TreeDist, TreeSearch, treespace, TreeTools |
| Reverse suggests: | CongreveLamsdell2016, gromovlab, mcbette, MicrobiotaProcess, msa, pagoo, Quartet, RRphylo, shipunov, tracerer, treeio |
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