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: | 2.5.5 |
| 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, vdiffr, seqinr, xtable, rgl, knitr, rmarkdown, Biostrings |
| Published: | 2019-06-19 |
| 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] |
| 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: |
Ancestral Sequence Reconstruction Constructing phylogenetic trees Advanced features IntertwiningTreesAndNetworks Splits and Networx |
| Package source: | phangorn_2.5.5.tar.gz |
| Windows binaries: | r-devel: phangorn_2.5.5.zip, r-release: phangorn_2.5.5.zip, r-oldrel: phangorn_2.5.5.zip |
| macOS binaries: | r-release: phangorn_2.5.5.tgz, r-oldrel: phangorn_2.5.5.tgz |
| Old sources: | phangorn archive |
| Reverse depends: | apex, MSCquartets, phybreak |
| Reverse imports: | BoSSA, BSS, coalescentMCMC, CommT, corHMM, dispRity, genBaRcode, haplotypes, indelmiss, ips, liayson, LymphoSeq, markophylo, MicrobiotaProcess, OUwie, paleotree, pcmabc, philr, phyloregion, phytools, poppr, RAM, recluster, rwty, selac, SeqFeatR, strataG, STraTUS, taxize, timetree, TreeDist, TreeSearch, treespace, TreeTools |
| Reverse suggests: | CongreveLamsdell2016, msa, Quartet, RRphylo, shipunov, tracerer, treeio |
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