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.


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:


See phyclust/inst/Documents/ for files in src/msdir/, src/seq-gen/, src/paml_baseml, and R/ttzeng-*.r.