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
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phyclust.pdf |phyclust.html✨
phyclust/json (API)

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

Peer review:

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

Datasets:
  • .Color - Colors for Identifying Clusters in Plots
  • .EMC - EM Control
  • .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
  • .edist.model - Evolution Distance Model
  • .em.method - EM Methods and Algorithms
  • .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:

134 exports 9 stars 3.56 score 5 dependencies 7 dependents 12 mentions 124 scripts 2.0k downloads

Last updated 1 years agofrom:3f82c7bc4f. Checks:OK: 1 WARNING: 8. Indexed: no.

TargetResultDate
Doc / VignettesOKAug 11 2024
R-4.5-win-x86_64WARNINGAug 11 2024
R-4.5-linux-x86_64WARNINGAug 11 2024
R-4.4-win-x86_64WARNINGAug 11 2024
R-4.4-mac-x86_64WARNINGAug 11 2024
R-4.4-mac-aarch64WARNINGAug 11 2024
R-4.3-win-x86_64WARNINGAug 11 2024
R-4.3-mac-x86_64WARNINGAug 11 2024
R-4.3-mac-aarch64WARNINGAug 11 2024

Exports:.EMControl.show.optionacode2aidacode2aid.defaultacode2aid.listaid2acodeaid2acode.defaultaid2acode.listas.star.treebootstrap.merge.seqbootstrap.seqbootstrap.seq.databootstrap.seq.nucleotidebootstrap.seq.snpbootstrap.star.treebootstrap.star.treesbootstrap.star.trees.seqcheck.EMCcheck.labelchkdim.Add.funchkdim.Multiply.funcid2aidcid2aid.defaultcid2aid.listcode2nidcode2nid.defaultcode2nid.listcode2snpcode2snp.defaultcode2snp.listconstruct.bigB.dPIconstruct.dB.list.funconvert.QA.to.vectfinal.BigMatB.funfinal.BigMatB.matC.funfind.bestfind.consensusgen.equal.star.anc.decgen.seq.HKYgen.seq.SNPgen.star.treegen.unit.Kget.allpossROUTE.funget.BB.funget.deriBigMatB.funget.fullBB.funget.I.funget.ini.possHap.hapReserv.funget.medBB.skip.funget.preBB.skip.funget.rooted.tree.heightget.step.mut.funget.subPI.fungetBigMatB.fungetcut.fungetI13.fungetPIstar.funhaplo.phase.knownhaplo.post.probI33Inv.funindex.k.funmsmy.catmy.formatmy.printnid2aidnid2aid.defaultnid2aid.listnid2cidnid2cid.defaultnid2cid.listnid2codenid2code.defaultnid2code.listnid2sidpaml.basemlpaml.baseml.controlpaml.baseml.show.defaultphyclustphyclust.e.stepphyclust.edistphyclust.em.stepphyclust.logLphyclust.m.stepphyclust.Ptphyclust.sephyclust.se.updatephyclust.updateplotdotsplotfdplotgapsplothistplothist.myplotnjplotstructprint.basemlprint.msprint.phyclustprint.Ptprint.RRandprint.seq.dataprint.seqgenprune.Muread.fastaread.fasta.formatread.phylipread.phylip.formatread.seqgenrescale.rooted.treeRRandseqgensid2nidsid2snpsid2snp.defaultsid2snp.listsnp2codesnp2code.defaultsnp2code.listsnp2sidsnp2sid.defaultsnp2sid.listsummary.phyclusttranslate.EMCtranslate.EMC.setranslate.rettranslate.ret.seunstrsplitwrite.fastawrite.fasta.formatwrite.pamlwrite.paml.formatwrite.phylipwrite.phylip.formatzero.mat.fun

Dependencies:apedigestlatticenlmeRcpp

phyclust-guide

Rendered fromphyclust-guide.Rnwusingutils::Sweaveon Aug 11 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Phyloclustering - Phylogenetic Clusteringphyclust-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 phyloas.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 / sidscode2snp nid2sid sid2nid snp2code
Great Pony 625 EIAV rev Dataset in the Fasta FormatData Pony 625 Format fasta
Crohn's Disease SNP Dataset in the phylip FormatData Crohn's Disease
Great Pony 524 EIAV rev Dataset in the phylip FormatData Pony 524 Format phylip
Read Data from Files by Formats and Return a seq.data Objectread.fasta read.fasta.format read.phylip read.phylip.format
Write Data to Files by Formatswrite.fasta write.fasta.format write.paml write.paml.format write.phylip write.phylip.format
Find the Best Solution of phyclustfind.best
Find the Consensus Sequencefind.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 Shapegen.star.tree
Generate Comprehensive Trees.gen.unit.K
Get a Rooted Tree Heightget.rooted.tree.height
Tzeng's Method: Finding the Best Number of Clustersgetcut.fun
Tzeng's Method: Haplotype Grouping for SNP Sequenceshaplo.post.prob
Generating Samples under a Wright-Fisher Neutral Model of Genetic VariationClass 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 SequencesClass baseml paml.baseml paml.baseml.control paml.baseml.show.default
The Main Function of phyclustClass phyclust phyclust
One E-Step of phyclustphyclust.e.step
Evolution Distance of Sequencesphyclust.edist
One EM-step of phyclustphyclust.em.step
Log-Likelihood of phyclustphyclust.logL
One M-Step of phyclustphyclust.m.step
Transition Probabilities of phyclust Given Timephyclust.Pt
The Main Function of phyclust for Sequencing Error Modelsphyclust.se
Update phyclust Results by the Sequencing Error Modelphyclust.se.update
Update phyclust Resultsphyclust.update
Dots Plots of Sequences for Visual Comparisonsplotdots
Gaps Plots of Sequences for Visual Comparisonsplotgaps
Plot Histogram to Compare Number of Mutations.plothist
Plot an Unrooted Trees.plotnj
Struct Plots of Observations Based on Posterior Probabilitiesplotstruct
Functions for Printing or Summarizing Objects According to Classesprint.baseml print.ms print.phyclust print.Pt print.RRand print.seq.data print.seqgen summary.phyclust
Prune the Center Sequences Muprune.Mu
Read seqgen's Results and Return a seq.dataread.seqgen
Rescale a Rooted Tree's Heightrescale.rooted.tree
Rand Index and Adjusted Rand IndexRRand
A Toy Dataset in Class seq.dataClass seq.data Data Toy seq.data.gap seq.data.toy
Seq-GenClass 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