phyclust

Phylogenetic Clustering (Phyloclustering)

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.

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Description file content

Package
phyclust
Version
0.1-28
Date
2019-12-01
Title
Phylogenetic Clustering (Phyloclustering)
Depends
R (>= 3.0.0), ape
LazyLoad
yes
LazyData
yes
Copyright
See phyclust/inst/Documents/ for files in src/msdir/, src/seq-gen/, src/paml_baseml, and R/ttzeng-*.r.
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.
BugReports
https://github.com/snoweye/phyclust/issues
License
GPL (>= 2)
URL
NeedsCompilation
yes
Maintainer
Wei-Chen Chen
Packaged
2019-12-01 20:55:09 UTC; snoweye
Author
Wei-Chen Chen [aut, cre], Karin Dorman [aut], Yan-Han Chen [ctb]
Repository
CRAN
Date/Publication
2019-12-08 10:30:07 UTC

install.packages('phyclust')

0.1-28

7 days ago

http://snoweye.github.io/phyclust/

Wei-Chen Chen

GPL (>= 2)

Depends on

R (>= 3.0.0), ape

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