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.
Version: | 0.1-16 |
Depends: | R (≥ 3.0.0), ape |
Published: | 2015-12-04 |
Author: | Wei-Chen Chen [aut, cre], Karin Dorman [aut] |
Maintainer: | Wei-Chen Chen <wccsnow at gmail.com> |
BugReports: | https://github.com/snoweye/phyclust/issues |
License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
Copyright: | See phyclust/inst/Documents/ for files in src/msdir/, src/seq-gen/, src/paml_baseml, and R/ttzeng-*.r. |
URL: | http://thirteen-01.stat.iastate.edu/snoweye/phyclust/ |
NeedsCompilation: | yes |
Citation: | phyclust citation info |
Materials: | ChangeLog |
In views: | Phylogenetics |
CRAN checks: | phyclust results |
Reference manual: | phyclust.pdf |
Vignettes: |
phyclust-guide |
Package source: | phyclust_0.1-16.tar.gz |
Windows binaries: | r-devel: phyclust_0.1-16.zip, r-release: phyclust_0.1-16.zip, r-oldrel: phyclust_0.1-16.zip |
OS X Snow Leopard binaries: | r-release: phyclust_0.1-16.tgz, r-oldrel: phyclust_0.1-15.tgz |
OS X Mavericks binaries: | r-release: phyclust_0.1-16.tgz |
Old sources: | phyclust archive |
Reverse suggests: | coala |
Reverse enhances: | pbdDEMO |