Phylogenetic Reconstruction and Analysis R package phangorn version 2.12.1 CRAN Task View: Phylogenetics (https://CRAN.R-project.org/view=Phylogenetics) 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). Software 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 Klaus Schliep <klaus.schliep@gmail.com> Comprehensive R Archive Network (CRAN) Klaus Schliep [aut, cre] (ORCID: <https://orcid.org/0000-0003-2941-0161>), Emmanuel Paradis [aut] (ORCID: <https://orcid.org/0000-0003-3092-2199>), Leonardo de Oliveira Martins [aut] (ORCID: <https://orcid.org/0000-0001-5247-1320>), Alastair Potts [aut], Iris Bardel-Kahr [aut] (ORCID: <https://orcid.org/0000-0002-8950-834X>), 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] (ORCID: <https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [ctb] (ORCID: <https://orcid.org/0000-0002-8926-5974>) GPL (>= 2) 2024-09-17 application/tgz https://CRAN.R-project.org/package=phangorn doi:10.32614/CRAN.package.phangorn en-US