DESCRIPTION

Package: phyclust
Version: 0.1-34
Date: 2023-09-03
Title: Phylogenetic Clustering (Phyloclustering)
Authors@R: c(person("Wei-Chen", "Chen", role = c("aut", "cre"), email =
        "wccsnow@gmail.com"), person("Karin", "Dorman", role =
        "aut"), person("Yan-Han", "Chen", role = "ctb"))
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) <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.
BugReports: https://github.com/snoweye/phyclust/issues
License: GPL (>= 2)
URL: https://snoweye.github.io/phyclust/
NeedsCompilation: yes
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>