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>
Repository: https://phylotastic.r-universe.dev
Date/Publication: 2023-09-06 02:49:02 UTC
RemoteUrl: https://github.com/snoweye/phyclust
RemoteRef: HEAD
RemoteSha: 3f82c7bc4f328ba3b07f50cd82eb09997f00fc17
Packaged: 2026-06-23 23:44:50 UTC; root
Author: Wei-Chen Chen [aut, cre],
  Karin Dorman [aut],
  Yan-Han Chen [ctb]