Wei-Chen Chen, Karin S. Dorman, Ranjan Maitra

Phylogenetic clustering (phyloclustering) is an evolutionary
Continuous Time Markov Chain model-based approach to identify
population structure from molecular data without assuming
linkage equilibrium. It 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 software, ms, seq-gen and Hap-Clustering for simulating
data and additional analyses. See the phyclust website for more
information, documentations and examples.

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.

c(person("Wei-Chen", "Chen", role = c("aut", "cre"), email =
"wccsnow@gmail.com"), person("Karin", "Dorman", role = "aut"))
Wei-Chen Chen [aut, cre], Karin Dorman [aut]

c(person("Wei-Chen", "Chen", role = c("aut", "cre"), email =
"wccsnow@gmail.com"), person("Karin", "Dorman", role =
"aut"))
See phyclust/inst/Documents/ for files in src/msdir/,
src/seq-gen/, src/paml_baseml, and R/ttzeng-*.r.
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.
Wei-Chen Chen [aut, cre],
Karin Dorman [aut]