Package: phyclust 0.1-34
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.
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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')) |
Bug tracker:https://github.com/snoweye/phyclust/issues
- .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
Last updated 1 years agofrom:3f82c7bc4f. Checks:OK: 1 WARNING: 8. Indexed: no.
Target | Result | Date |
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Doc / Vignettes | OK | Aug 11 2024 |
R-4.5-win-x86_64 | WARNING | Aug 11 2024 |
R-4.5-linux-x86_64 | WARNING | Aug 11 2024 |
R-4.4-win-x86_64 | WARNING | Aug 11 2024 |
R-4.4-mac-x86_64 | WARNING | Aug 11 2024 |
R-4.4-mac-aarch64 | WARNING | Aug 11 2024 |
R-4.3-win-x86_64 | WARNING | Aug 11 2024 |
R-4.3-mac-x86_64 | WARNING | Aug 11 2024 |
R-4.3-mac-aarch64 | WARNING | Aug 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