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), seq-gen (Rambaut and Grassly 1997), Hap-Clustering (Tzeng 2005) and PAML baseml (Yang 1997, 2007), for simulating data, additional analyses, and searching the best tree. See the phyclust website for more information, documentations and examples.

Version: 0.1-15
Depends: R (≥ 2.14.0), ape
Published: 2013-12-14
Author: Wei-Chen Chen [aut, cre], Karin Dorman [aut]
Maintainer: Wei-Chen Chen <wccsnow at gmail.com>
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: http://thirteen-01.stat.iastate.edu/snoweye/phyclust/
NeedsCompilation: yes
Citation: phyclust citation info
Materials: ChangeLog
In views: Phylogenetics
CRAN checks: phyclust results

Downloads:

Reference manual: phyclust.pdf
Vignettes: phyclust-guide
Package source: phyclust_0.1-15.tar.gz
Windows binaries: r-devel: phyclust_0.1-15.zip, r-release: phyclust_0.1-15.zip, r-oldrel: phyclust_0.1-15.zip
OS X Snow Leopard binaries: r-release: phyclust_0.1-15.tgz, r-oldrel: phyclust_0.1-15.tgz
OS X Mavericks binaries: r-release: phyclust_0.1-15.tgz
Old sources: phyclust archive

Reverse dependencies:

Reverse imports: jaatha
Reverse enhances: pbdDEMO