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
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: