phyclust (version 0.1-11)
Phylogenetic Clustering (Phyloclustering)
Description
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.