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phyclust
View on CRAN: Click
here
Download and install phyclust package within the R console
Install from CRAN:
install.packages("phyclust")
Install from Github:
library("remotes")
install_github("cran/phyclust")
Install by package version:
library("remotes")
install_version("phyclust", "0.1-34")
Attach the package and use:
library("phyclust")
Maintained by
Wei-Chen Chen
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2010-01-29
Latest Update: 2023-09-06
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.
How to cite:
Wei-Chen Chen (2010). phyclust: Phylogenetic Clustering (Phyloclustering). R package version 0.1-34, https://cran.r-project.org/web/packages/phyclust
Previous versions and publish date:
0.1-1 (2010-01-29 08:53), 0.1-2 (2010-02-18 17:53), 0.1-3 (2010-02-19 15:44), 0.1-4 (2010-02-21 19:43), 0.1-5 (2010-02-22 09:05), 0.1-6 (2010-04-10 08:33), 0.1-7 (2010-04-27 21:10), 0.1-8 (2010-09-19 20:30), 0.1-9 (2011-10-26 20:00), 0.1-10 (2011-11-06 09:39), 0.1-11 (2012-03-11 07:35), 0.1-12 (2012-06-06 08:05), 0.1-13 (2012-12-26 09:25), 0.1-14 (2013-01-08 19:18), 0.1-15 (2013-12-14 20:31), 0.1-16 (2015-12-04 08:40), 0.1-17 (2016-07-15 10:14), 0.1-18 (2016-12-11 12:26), 0.1-19 (2017-04-29 23:20), 0.1-20 (2017-08-26 15:27), 0.1-21 (2017-11-18 19:58), 0.1-22 (2017-12-02 20:22), 0.1-23 (2019-03-08 14:50), 0.1-24 (2019-03-27 11:00), 0.1-25 (2019-08-25 11:20), 0.1-26 (2019-09-27 06:30), 0.1-27 (2019-11-29 13:00), 0.1-28 (2019-12-08 11:30), 0.1-29 (2020-05-11 19:00), 0.1-30 (2021-02-10 15:00), 0.1-32 (2022-10-25 08:22), 0.1-33 (2023-01-22 22:40)
Other packages that cited phyclust R package
View phyclust citation profile
Other R packages that phyclust depends,
imports, suggests or enhances
Functions, R codes and Examples using
the phyclust R package
Some associated functions: 00_phyclust-package . 11_d.Color . 11_d.EMC . 11_d.EMControl . 11_d.boundary.method . 11_d.code.type . 11_d.edist.model . 11_d.em.method . 11_d.identifier . 11_d.init.method . 11_d.init.procedure . 11_d.label.method . 11_d.se.model . 11_d.show.option . 11_d.standard.code . 11_d.substitution . RRand . as.star.tree . bootstrap.seq.data . bootstrap.seq . bootstrap.star.trees . bootstrap.star.trees.seq . code2nid . code2snp . data.fasta.pony . data.phylip.crohn . data.phylip.pony . file.read . file.write . find.best . find.consensus . gen.equal.star.anc.dec . gen.seq . gen.star.tree . gen.unit.K . get.rooted.tree.height . getcut.fun . haplo.post.prob . ms . nid.aid.cid . paml.baseml . phyclust.Pt . phyclust.e.step . phyclust.edist . phyclust.em.step . phyclust.logL . phyclust.m.step . phyclust . phyclust.se . phyclust.se.update . phyclust.update . plotdots . plotgaps . plothist . plotnj . plotstruct . print.summary . prune.Mu . read.seqgen . rescale.rooted.tree . seq.data . seqgen . snp2sid . zz_all.internal . zz_all.internal.tzeng .
Some associated R codes: Full phyclust package functions and examples
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