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phyclust
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Phylogenetic Clustering (Phyloclustering)
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phyclust
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# phyclust * **License:** [](http://www.gnu.org/licenses/gpl-2.0.en.html) * **Download:** [](https://cran.r-project.org/package=phyclust) * **Author:** Wei-Chen Chen and Karin Dorman 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. ## Installation phyclust requires * R version 3.0.0 or higher. * R package ape. The package can be installed from the CRAN via the usual `install.packages("phyclust")`, or via the devtools package: ```r library(devtools) install_github("snoweye/phyclust") ``` ## Copyright See phyclust/inst/Documents/ for files in src/msdir/, src/seq-gen/, src/paml_baseml, and R/ttzeng-*.r.
