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) doi:10.1093/bioinformatics/18.2.337, seq-gen (Rambaut and Grassly 1997) doi:10.1093/bioinformatics/13.3.235, Hap-Clustering (Tzeng 2005) doi:10.1002/gepi.20063 and PAML baseml (Yang 1997, 2007) doi:10.1093/bioinformatics/13.5.555, doi:10.1093/molbev/msm088, for simulating data, additional analyses, and searching the best tree. See the phyclust website for more information, documentations and examples.