phyclust

Phylogenetic Clustering (Phyloclustering)

Last update: 6 September 2023

Software version identifier: 0.1-33, 0.1-1, 0.1-2, 0.1-3, 0.1-4, 0.1-5, 0.1-6, 0.1-7, 0.1-8, 0.1-9, 0.1-10, 0.1-11, 0.1-12, 0.1-13, 0.1-14, 0.1-15, 0.1-16, 0.1-17, 0.1-18, 0.1-19, 0.1-20, 0.1-21, 0.1-22, 0.1-23, 0.1-24, 0.1-25, 0.1-26, 0.1-27, 0.1-28, 0.1-29, 0.1-30, 0.1-32, 0.1-34

Source code repository: https://github.com/cran/phyclust

Copyright license: GNU General Public License, version 3.0, GNU General Public License, version 2.0

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) <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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