This package is considered a duplicate. The official version of this package is found at:https://snoweye.r-universe.dev/phyclust

Package: phyclust 0.1-34

Wei-Chen Chen

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.

Authors:Wei-Chen Chen [aut, cre], Karin Dorman [aut], Yan-Han Chen [ctb]

phyclust_0.1-34.tar.gz
phyclust_0.1-34.zip(r-4.7)phyclust_0.1-34.zip(r-4.6)phyclust_0.1-34.zip(r-4.5)
phyclust_0.1-34.tgz(r-4.6-x86_64)phyclust_0.1-34.tgz(r-4.6-arm64)phyclust_0.1-34.tgz(r-4.5-x86_64)phyclust_0.1-34.tgz(r-4.5-arm64)
phyclust_0.1-34.tar.gz(r-4.7-arm64)phyclust_0.1-34.tar.gz(r-4.7-x86_64)phyclust_0.1-34.tar.gz(r-4.6-arm64)phyclust_0.1-34.tar.gz(r-4.6-x86_64)
phyclust_0.1-34.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
phyclust/json (API)

# Install 'phyclust' in R:

install.packages('phyclust', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/snoweye/phyclust/issues

Datasets:

.amino.acid - Standard Codes and ids for Nucleotides, SNPs, Codon, Amino Acid and Genetic Code
.boundary.method - Boundary Methods for Population Proportions
.code.type - Code Types of Dataset and Substitution Models
.codon - Standard Codes and ids for Nucleotides, SNPs, Codon, Amino Acid and Genetic Code
.Color - Colors for Identifying Clusters in Plots
.edist.model - Evolution Distance Model
.em.method - EM Methods and Algorithms
.EMC - EM Control
.genetic.code - Standard Codes and ids for Nucleotides, SNPs, Codon, Amino Acid and Genetic Code
.identifier - Identifiers for Evolution Models
.init.method - Initialization Methods for EM Algorithms
.init.procedure - Initialization Procedures for EM Algorithms
.label.method - Label Method
.missing.code - Standard Codes and ids for Nucleotides, SNPs, Codon, Amino Acid and Genetic Code
.nucleotide - Standard Codes and ids for Nucleotides, SNPs, Codon, Amino Acid and Genetic Code
.se.model - Sequencing Error Model
.snp - Standard Codes and ids for Nucleotides, SNPs, Codon, Amino Acid and Genetic Code
.substitution.model - Substitution Models for Mutation Processes
seq.data.gap - A Toy Dataset in Class seq.data
seq.data.toy - A Toy Dataset in Class seq.data

On CRAN:

8.82 score 10 stars 8 packages 237 scripts 2.3k downloads 12 mentions 134 exports 5 dependencies

Last updated from:3f82c7bc4f. Checks:11 WARNING, 2 OK. Indexed: no.

Target	Result	Time
linux-devel-arm64	WARNING	154
linux-devel-x86_64	WARNING	204
source / vignettes	OK	275
linux-release-arm64	WARNING	149
linux-release-x86_64	WARNING	147
macos-release-arm64	WARNING	89
macos-release-x86_64	WARNING	285
macos-oldrel-arm64	WARNING	90
macos-oldrel-x86_64	WARNING	302
windows-devel	WARNING	148
windows-release	WARNING	115
windows-oldrel	WARNING	123
wasm-release	OK	169

Exports:.EMControl .show.option acode2aid acode2aid.default acode2aid.list aid2acode aid2acode.default aid2acode.list as.star.tree bootstrap.merge.seq bootstrap.seq bootstrap.seq.data bootstrap.seq.nucleotide bootstrap.seq.snp bootstrap.star.tree bootstrap.star.trees bootstrap.star.trees.seq check.EMC check.label chkdim.Add.fun chkdim.Multiply.fun cid2aid cid2aid.default cid2aid.list code2nid code2nid.default code2nid.list code2snp code2snp.default code2snp.list construct.bigB.dPI construct.dB.list.fun convert.QA.to.vect final.BigMatB.fun final.BigMatB.matC.fun find.best find.consensus gen.equal.star.anc.dec gen.seq.HKY gen.seq.SNP gen.star.tree gen.unit.K get.allpossROUTE.fun get.BB.fun get.deriBigMatB.fun get.fullBB.fun get.I.fun get.ini.possHap.hapReserv.fun get.medBB.skip.fun get.preBB.skip.fun get.rooted.tree.height get.step.mut.fun get.subPI.fun getBigMatB.fun getcut.fun getI13.fun getPIstar.fun haplo.phase.known haplo.post.prob I33Inv.fun index.k.fun ms my.cat my.format my.print nid2aid nid2aid.default nid2aid.list nid2cid nid2cid.default nid2cid.list nid2code nid2code.default nid2code.list nid2sid paml.baseml paml.baseml.control paml.baseml.show.default phyclust phyclust.e.step phyclust.edist phyclust.em.step phyclust.logL phyclust.m.step phyclust.Pt phyclust.se phyclust.se.update phyclust.update plotdots plotfd plotgaps plothist plothist.my plotnj plotstruct print.baseml print.ms print.phyclust print.Pt print.RRand print.seq.data print.seqgen prune.Mu read.fasta read.fasta.format read.phylip read.phylip.format read.seqgen rescale.rooted.tree RRand seqgen sid2nid sid2snp sid2snp.default sid2snp.list snp2code snp2code.default snp2code.list snp2sid snp2sid.default snp2sid.list summary.phyclust translate.EMC translate.EMC.se translate.ret translate.ret.se unstrsplit write.fasta write.fasta.format write.paml write.paml.format write.phylip write.phylip.format zero.mat.fun

Dependencies:ape digest lattice nlme Rcpp

phyclust-guide

Rendered fromphyclust-guide.Rnwusingutils::Sweave

Last update: 2021-02-10
Started: 2013-07-03

Help page	Topics
Phyloclustering - Phylogenetic Clustering	phyclust-package
Boundary Methods for Population Proportions	.boundary.method
Code Types of Dataset and Substitution Models	.code.type
Colors for Identifying Clusters in Plots	.Color
Evolution Distance Model	.edist.model
EM Methods and Algorithms	.em.method
EM Control	.EMC
EM Control Generator	.EMControl
Identifiers for Evolution Models	.identifier
Initialization Methods for EM Algorithms	.init.method
Initialization Procedures for EM Algorithms	.init.procedure
Label Method	.label.method
Sequencing Error Model	.se.model
Show Available Options	.show.option
Substitution Models for Mutation Processes	.substitution.model
Coerce a Rooted Tree to a Star Tree in Class phylo	as.star.tree Class phylo
Bootstrap Sequences from a Fitted Model and Star Tree.	bootstrap.seq
Bootstrap a seq.data from a Fitted Model.	bootstrap.seq.data
Bootstrap a Star Tree from a Fitted Model.	bootstrap.star.trees
Bootstrap Sequences from a Fitted Model.	bootstrap.star.trees.seq
Transfer Codes (A, G, C, T, -) and nids (0, 1, 2, 3, 4)	code2nid nid2code
Transfer Nucleotide Codes / nids and SNPs / sids	code2snp nid2sid sid2nid snp2code
Great Pony 625 EIAV rev Dataset in the Fasta Format	Data Pony 625 Format fasta
Crohn's Disease SNP Dataset in the phylip Format	Data Crohn's Disease
Great Pony 524 EIAV rev Dataset in the phylip Format	Data Pony 524 Format phylip
Read Data from Files by Formats and Return a seq.data Object	read.fasta read.fasta.format read.phylip read.phylip.format
Write Data to Files by Formats	write.fasta write.fasta.format write.paml write.paml.format write.phylip write.phylip.format
Find the Best Solution of phyclust	find.best
Find the Consensus Sequence	find.consensus
Generate Comprehensive Trees.	gen.equal.star.anc.dec
Generate Sequences Given a Rooted Tree.	gen.seq.HKY gen.seq.SNP
Generate a Rooted Tree with a Star Shape	gen.star.tree
Generate Comprehensive Trees.	gen.unit.K
Get a Rooted Tree Height	get.rooted.tree.height
Tzeng's Method: Finding the Best Number of Clusters	getcut.fun
Tzeng's Method: Haplotype Grouping for SNP Sequences	haplo.post.prob
Generating Samples under a Wright-Fisher Neutral Model of Genetic Variation	Class ms ms
Transfer nids (0, 1, ..., 4) , aids (0, 1, ..., 21) and cids (0, 1, ..., 64)	acode2aid aid2acode cid2aid nid2aid nid2cid
Phylogenetic Analysis by Maximum Likelihood for Nucleotide Sequences	Class baseml paml.baseml paml.baseml.control paml.baseml.show.default
The Main Function of phyclust	Class phyclust phyclust
One E-Step of phyclust	phyclust.e.step
Evolution Distance of Sequences	phyclust.edist
One EM-step of phyclust	phyclust.em.step
Log-Likelihood of phyclust	phyclust.logL
One M-Step of phyclust	phyclust.m.step
Transition Probabilities of phyclust Given Time	phyclust.Pt
The Main Function of phyclust for Sequencing Error Models	phyclust.se
Update phyclust Results by the Sequencing Error Model	phyclust.se.update
Update phyclust Results	phyclust.update
Dots Plots of Sequences for Visual Comparisons	plotdots
Gaps Plots of Sequences for Visual Comparisons	plotgaps
Plot Histogram to Compare Number of Mutations.	plothist
Plot an Unrooted Trees.	plotnj
Struct Plots of Observations Based on Posterior Probabilities	plotstruct
Functions for Printing or Summarizing Objects According to Classes	print.baseml print.ms print.phyclust print.Pt print.RRand print.seq.data print.seqgen summary.phyclust
Prune the Center Sequences Mu	prune.Mu
Read seqgen's Results and Return a seq.data	read.seqgen
Rescale a Rooted Tree's Height	rescale.rooted.tree
Rand Index and Adjusted Rand Index	RRand
A Toy Dataset in Class seq.data	Class seq.data Data Toy seq.data.gap seq.data.toy
Seq-Gen	Class seqgen seqgen
Transfer SNP codes (1, 2, -) and sids (0, 1, 2)	sid2snp snp2sid
Standard Codes and ids for Nucleotides, SNPs, Codon, Amino Acid and Genetic Code	.amino.acid .codon .genetic.code .missing.code .nucleotide .snp

Package: phyclust 0.1-34

phyclust: Phylogenetic Clustering (Phyloclustering)

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