Man pages for snoweye/phyclust
Phylogenetic Clustering (Phyloclustering)

00_phyclust-packagePhyloclustering - Phylogenetic Clustering
11_d.boundary.methodBoundary Methods for Population Proportions
11_d.code.typeCode Types of Dataset and Substitution Models
11_d.ColorColors for Identifying Clusters in Plots
11_d.edist.modelEvolution Distance Model
11_d.EMCEM Control
11_d.EMControlEM Control Generator
11_d.em.methodEM Methods and Algorithms
11_d.identifierIdentifiers for Evolution Models
11_d.init.methodInitialization Methods for EM Algorithms
11_d.init.procedureInitialization Procedures for EM Algorithms
11_d.label.methodLabel Method
11_d.se.modelSequencing Error Model
11_d.show.optionShow Available Options
11_d.standard.codeStandard Codes and ids for Nucleotides, SNPs, Codon, Amino...
11_d.substitutionSubstitution Models for Mutation Processes
as.star.treeCoerce a Rooted Tree to a Star Tree in Class phylo
bootstrap.seqBootstrap Sequences from a Fitted Model and Star Tree.
bootstrap.seq.dataBootstrap a seq.data from a Fitted Model.
bootstrap.star.treesBootstrap a Star Tree from a Fitted Model.
bootstrap.star.trees.seqBootstrap Sequences from a Fitted Model.
code2nidTransfer Codes (A, G, C, T, -) and nids (0, 1, 2, 3, 4)
code2snpTransfer Nucleotide Codes / nids and SNPs / sids
data.fasta.ponyGreat Pony 625 EIAV rev Dataset in the Fasta Format
data.phylip.crohnCrohn's Disease SNP Dataset in the phylip Format
data.phylip.ponyGreat Pony 524 EIAV rev Dataset in the phylip Format
file.readRead Data from Files by Formats and Return a seq.data Object
file.writeWrite Data to Files by Formats
find.bestFind the Best Solution of phyclust
find.consensusFind the Consensus Sequence
gen.equal.star.anc.decGenerate Comprehensive Trees.
gen.seqGenerate Sequences Given a Rooted Tree.
gen.star.treeGenerate a Rooted Tree with a Star Shape
gen.unit.KGenerate Comprehensive Trees.
getcut.funTzeng's Method: Finding the Best Number of Clusters
get.rooted.tree.heightGet a Rooted Tree Height
haplo.post.probTzeng's Method: Haplotype Grouping for SNP Sequences
msGenerating Samples under a Wright-Fisher Neutral Model of...
nid.aid.cidTransfer nids (0, 1, ..., 4) , aids (0, 1, ..., 21) and cids...
paml.basemlPhylogenetic Analysis by Maximum Likelihood for Nucleotide...
phyclustThe Main Function of phyclust
phyclust.edistEvolution Distance of Sequences
phyclust.em.stepOne EM-step of phyclust
phyclust.e.stepOne E-Step of phyclust
phyclust.logLLog-Likelihood of phyclust
phyclust.m.stepOne M-Step of phyclust
phyclust.PtTransition Probabilities of phyclust Given Time
phyclust.seThe Main Function of phyclust for Sequencing Error Models
phyclust.se.updateUpdate phyclust Results by the Sequencing Error Model
phyclust.updateUpdate phyclust Results
plotdotsDots Plots of Sequences for Visual Comparisons
plotgapsGaps Plots of Sequences for Visual Comparisons
plothistPlot Histogram to Compare Number of Mutations.
plotnjPlot an Unrooted Trees.
plotstructStruct Plots of Observations Based on Posterior Probabilities
print.summaryFunctions for Printing or Summarizing Objects According to...
prune.MuPrune the Center Sequences Mu
read.seqgenRead seqgen's Results and Return a seq.data
rescale.rooted.treeRescale a Rooted Tree's Height
RRandRand Index and Adjusted Rand Index
seq.dataA Toy Dataset in Class seq.data
seqgenSeq-Gen
snp2sidTransfer SNP codes (1, 2, -) and sids (0, 1, 2)
zz_all.internalAll Internal Functions of phyclust
zz_all.internal.tzengAll Internal Functions of Tzeng's Methods
snoweye/phyclust documentation built on Feb. 4, 2018, 1:06 a.m.