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 gmail.com>
BugReports:	https://github.com/snoweye/phyclust/issues
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.
URL:	https://snoweye.github.io/phyclust/
NeedsCompilation:	yes
Citation:	phyclust citation info
Materials:	README ChangeLog
In views:	Phylogenetics
CRAN checks:	phyclust results

Documentation:

Reference manual:	phyclust.pdf
Vignettes:	phyclust-guide

Downloads:

Package source:	phyclust_0.1-34.tar.gz
Windows binaries:	r-devel: phyclust_0.1-34.zip, r-release: phyclust_0.1-34.zip, r-oldrel: phyclust_0.1-34.zip
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

Linking:

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