phyclust: Phylogenetic Clustering (Phyloclustering)

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.

Version: 0.1-34
Depends: R (≥ 3.0.0), ape
Published: 2023-09-06
DOI: 10.32614/CRAN.package.phyclust
Author: Wei-Chen Chen [aut, cre], Karin Dorman [aut], Yan-Han Chen [ctb]
Maintainer: Wei-Chen Chen <wccsnow at>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
Copyright: See phyclust/inst/Documents/ for files in src/msdir/, src/seq-gen/, src/paml_baseml, and R/ttzeng-*.r.
NeedsCompilation: yes
Citation: phyclust citation info
Materials: README ChangeLog
In views: Phylogenetics
CRAN checks: phyclust results


Reference manual: phyclust.pdf
Vignettes: phyclust-guide


Package source: phyclust_0.1-34.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): phyclust_0.1-34.tgz, r-oldrel (arm64): phyclust_0.1-34.tgz, r-release (x86_64): phyclust_0.1-34.tgz, r-oldrel (x86_64): phyclust_0.1-34.tgz
Old sources: phyclust archive

Reverse dependencies:

Reverse imports: biclustermd, dispRity, iNEXT.3D, iNEXT.beta3D, infercnv
Reverse suggests: coala


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