phyclust (0.1-28)

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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.

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

License: GPL (>= 2)

Uses: ape
Reverse depends: jaatha
Reverse suggests: coala
Reverse enhances: pbdDEMO

Released 4 months ago.

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Related packages: PHYLOGR, apTreeshape, geiger, ggplot2, ouch, paleoTS, rmetasim, vegan, ape, phangorn, picante, MCMCglmm, metafor, pegas, phylobase, adephylo, phyloclim, BoSSA, TreeSim, TreePar(20 best matches, based on common tags.)

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