{ "_id": "6ac785acde46216d5edd185f", "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 =\n\"wccsnow@gmail.com\"), person(\"Karin\", \"Dorman\", role =\n\"aut\"), person(\"Yan-Han\", \"Chen\", role = \"ctb\"))", "LazyLoad": "yes", "LazyData": "yes", "Copyright": "See phyclust/inst/Documents/ for files in src/msdir/,\nsrc/seq-gen/, src/paml_baseml, and R/ttzeng-*.r.", "Description": "Phylogenetic clustering (phyloclustering) is an\nevolutionary Continuous Time Markov Chain model-based approach\nto identify population structure from molecular data without\nassuming linkage equilibrium. The package phyclust (Chen 2011)\nprovides a convenient implementation of phyloclustering for DNA\nand SNP data, capable of clustering individuals into\nsubpopulations and identifying molecular sequences\nrepresentative of those subpopulations. It is designed in C for\nperformance, interfaced with R for visualization, and\nincorporates other popular open source programs including ms\n(Hudson 2002) , seq-gen\n(Rambaut and Grassly 1997)\n, Hap-Clustering (Tzeng\n2005) and PAML baseml (Yang 1997,\n2007) ,\n, for simulating data, additional\nanalyses, and searching the best tree. See the phyclust website\nfor 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 ", "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": { "Date": "2026-10-08 11:31:55 UTC", "User": "root" }, "Author": "Wei-Chen Chen [aut, cre],\nKarin Dorman [aut],\nYan-Han Chen [ctb]", "_user": "phylotastic", "_type": "src", "_file": "phyclust_0.1-34.tar.gz", "_fileid": "https://r2.ropensci.org/1a9f4ea2e67e268d97cf86eec211fad2a384240b08f0f9ec6922e2d3e71e58da", "_filesize": 1201087, "_sha256": "1a9f4ea2e67e268d97cf86eec211fad2a384240b08f0f9ec6922e2d3e71e58da", "_expires": "2027-01-16T11:59:38.000Z", "_created": 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Codon, Amino Acid and Genetic Code", "object": "stdcode", "class": [ "data.frame" ], "fields": [ "cid", "nid", "codon.code", "aid", "amino.acid.code" ], "rows": 64, "table": true, "tojson": true }, { "name": ".identifier", "title": "Identifiers for Evolution Models", "object": "control", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": ".init.method", "title": "Initialization Methods for EM Algorithms", "object": "control", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": ".init.procedure", "title": "Initialization Procedures for EM Algorithms", "object": "control", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": ".label.method", "title": "Label Method", "object": "control", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": ".missing.code", "title": "Standard Codes and ids for Nucleotides, SNPs, Codon, Amino Acid and Genetic Code", "object": 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Disease SNP Dataset in the phylip Format", "topics": [ "Data Crohn's Disease" ] }, { "page": "data.phylip.pony", "title": "Great Pony 524 EIAV rev Dataset in the phylip Format", "topics": [ "Data Pony 524", "Format phylip" ] }, { "page": "file.read", "title": "Read Data from Files by Formats and Return a seq.data Object", "topics": [ "read.fasta", "read.fasta.format", "read.phylip", "read.phylip.format" ] }, { "page": "file.write", "title": "Write Data to Files by Formats", "topics": [ "write.fasta", "write.fasta.format", "write.paml", "write.paml.format", "write.phylip", "write.phylip.format" ] }, { "page": "find.best", "title": "Find the Best Solution of phyclust", "topics": [ "find.best" ] }, { "page": "find.consensus", "title": "Find the Consensus Sequence", "topics": [ "find.consensus" ] }, { "page": "gen.equal.star.anc.dec", "title": "Generate Comprehensive Trees.", "topics": [ "gen.equal.star.anc.dec" ] }, { "page": "gen.seq", "title": "Generate Sequences Given a Rooted Tree.", 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}, { "page": "phyclust.se.update", "title": "Update phyclust Results by the Sequencing Error Model", "topics": [ "phyclust.se.update" ] }, { "page": "phyclust.update", "title": "Update phyclust Results", "topics": [ "phyclust.update" ] }, { "page": "plotdots", "title": "Dots Plots of Sequences for Visual Comparisons", "topics": [ "plotdots" ] }, { "page": "plotgaps", "title": "Gaps Plots of Sequences for Visual Comparisons", "topics": [ "plotgaps" ] }, { "page": "plothist", "title": "Plot Histogram to Compare Number of Mutations.", "topics": [ "plothist" ] }, { "page": "plotnj", "title": "Plot an Unrooted Trees.", "topics": [ "plotnj" ] }, { "page": "plotstruct", "title": "Struct Plots of Observations Based on Posterior Probabilities", "topics": [ "plotstruct" ] }, { "page": "print.summary", "title": "Functions for Printing or Summarizing Objects According to Classes", "topics": [ "print.baseml", "print.ms", "print.phyclust", "print.Pt", "print.RRand", "print.seq.data", "print.seqgen", "summary.phyclust" ] }, { "page": "prune.Mu", "title": "Prune the Center Sequences Mu", "topics": [ "prune.Mu" ] }, { "page": "read.seqgen", "title": "Read seqgen's Results and Return a seq.data", "topics": [ "read.seqgen" ] }, { "page": "rescale.rooted.tree", "title": "Rescale a Rooted Tree's Height", "topics": [ "rescale.rooted.tree" ] }, { "page": "RRand", "title": "Rand Index and Adjusted Rand Index", "topics": [ "RRand" ] }, { "page": "seq.data", "title": "A Toy Dataset in Class seq.data", "topics": [ "Class seq.data", "Data Toy", "seq.data.gap", "seq.data.toy" ] }, { "page": "seqgen", "title": "Seq-Gen", "topics": [ "Class seqgen", "seqgen" ] }, { "page": "snp2sid", "title": "Transfer SNP codes (1, 2, -) and sids (0, 1, 2)", "topics": [ "sid2snp", "snp2sid" ] }, { "page": "11_d.standard.code", "title": "Standard Codes and ids for Nucleotides, SNPs, Codon, Amino Acid and Genetic Code", "topics": [ ".amino.acid", ".codon", ".genetic.code", ".missing.code", ".nucleotide", ".snp" ] } 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