Phylogenetic Clustering (Phyloclustering) R package phyclust version 0.1-34 CRAN Task View: Phylogenetics (https://CRAN.R-project.org/view=Phylogenetics) Phylogenetic clustering (phyloclustering) is an evolutionary Continuous Time Markov Chain model-based approach to identify population structure from molecular data without assuming linkage equilibrium. The package phyclust (Chen 2011) provides a convenient implementation of phyloclustering for DNA and SNP data, capable of clustering individuals into subpopulations and identifying molecular sequences representative of those subpopulations. It is designed in C for performance, interfaced with R for visualization, and incorporates other popular open source programs including ms (Hudson 2002) <doi:10.1093/bioinformatics/18.2.337>, seq-gen (Rambaut and Grassly 1997) <doi:10.1093/bioinformatics/13.3.235>, Hap-Clustering (Tzeng 2005) <doi:10.1002/gepi.20063> and PAML baseml (Yang 1997, 2007) <doi:10.1093/bioinformatics/13.5.555>, <doi:10.1093/molbev/msm088>, for simulating data, additional analyses, and searching the best tree. See the phyclust website for more information, documentations and examples. Software Depends: R (>= 3.0.0), ape Wei-Chen Chen <wccsnow@gmail.com> Comprehensive R Archive Network (CRAN) Wei-Chen Chen [aut, cre], Karin Dorman [aut], Yan-Han Chen [ctb] GPL (>= 2) 2023-09-06 application/tgz https://CRAN.R-project.org/package=phyclust doi:10.32614/CRAN.package.phyclust