phyclust (0.1-14)

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Phylogenetic Clustering (Phyloclustering).

http://thirteen-01.stat.iastate.edu/snoweye/phyclust/
http://cran.r-project.org/web/packages/phyclust

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.

Maintainer: Wei-Chen Chen
Author(s): Wei-Chen Chen [aut, cre], Karin Dorman [aut]

License: GPL (>= 2)

Uses: ape
Reverse depends: jaatha

Released 4 months ago.

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