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