# Phylogenetic Clustering (Phyloclustering)

## Documentation for package ‘phyclust’ version 0.1-34

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Code demos. Use demo() to run them.
- Package README

## Help Pages

A B C D F G H M N P R S W misc

phyclust-package | Phyloclustering - Phylogenetic Clustering

## -- A --

acode2aid | Transfer nids (0, 1, ..., 4) , aids (0, 1, ..., 21) and cids (0, 1, ..., 64)
aid2acode | Transfer nids (0, 1, ..., 4) , aids (0, 1, ..., 21) and cids (0, 1, ..., 64)
as.star.tree | Coerce a Rooted Tree to a Star Tree in Class phylo

## -- B --

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.

## -- C --

cid2aid | Transfer nids (0, 1, ..., 4) , aids (0, 1, ..., 21) and cids (0, 1, ..., 64)
Class baseml | Phylogenetic Analysis by Maximum Likelihood for Nucleotide Sequences
Class ms | Generating Samples under a Wright-Fisher Neutral Model of Genetic Variation
Class phyclust | The Main Function of phyclust
Class phylo | Coerce a Rooted Tree to a Star Tree in Class phylo
Class seq.data | A Toy Dataset in Class seq.data
Class seqgen | Seq-Gen
code2nid | Transfer Codes (A, G, C, T, -) and nids (0, 1, 2, 3, 4)
code2snp | Transfer Nucleotide Codes / nids and SNPs / sids

## -- D --

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
Data Toy | A Toy Dataset in Class seq.data

## -- F --

find.best | Find the Best Solution of phyclust
find.consensus | Find the Consensus Sequence
Format fasta | Great Pony 625 EIAV rev Dataset in the Fasta Format
Format phylip | Great Pony 524 EIAV rev Dataset in the phylip Format

## -- G --

gen.equal.star.anc.dec | Generate Comprehensive Trees.
gen.seq.HKY | Generate Sequences Given a Rooted Tree.
gen.seq.SNP | 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

## -- H --

haplo.post.prob | Tzeng's Method: Haplotype Grouping for SNP Sequences

## -- M --

ms | Generating Samples under a Wright-Fisher Neutral Model of Genetic Variation

## -- N --

nid2aid | Transfer nids (0, 1, ..., 4) , aids (0, 1, ..., 21) and cids (0, 1, ..., 64)
nid2cid | Transfer nids (0, 1, ..., 4) , aids (0, 1, ..., 21) and cids (0, 1, ..., 64)
nid2code | Transfer Codes (A, G, C, T, -) and nids (0, 1, 2, 3, 4)
nid2sid | Transfer Nucleotide Codes / nids and SNPs / sids

## -- P --

paml.baseml | Phylogenetic Analysis by Maximum Likelihood for Nucleotide Sequences
paml.baseml.control | Phylogenetic Analysis by Maximum Likelihood for Nucleotide Sequences
paml.baseml.show.default | Phylogenetic Analysis by Maximum Likelihood for Nucleotide Sequences
phyclust | The Main Function of phyclust
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.Pt | Transition Probabilities of phyclust Given Time
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
print.ms | Functions for Printing or Summarizing Objects According to Classes
print.phyclust | Functions for Printing or Summarizing Objects According to Classes
print.Pt | Functions for Printing or Summarizing Objects According to Classes
print.RRand | Functions for Printing or Summarizing Objects According to Classes
print.seq.data | Functions for Printing or Summarizing Objects According to Classes
print.seqgen | Functions for Printing or Summarizing Objects According to Classes
prune.Mu | Prune the Center Sequences Mu

## -- R --

read.fasta | Read Data from Files by Formats and Return a seq.data Object
read.fasta.format | Read Data from Files by Formats and Return a seq.data Object
read.phylip | Read Data from Files by Formats and Return a seq.data Object
read.phylip.format | 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
RRand | Rand Index and Adjusted Rand Index

## -- S --

seq.data.gap | A Toy Dataset in Class seq.data
seq.data.toy | A Toy Dataset in Class seq.data
seqgen | Seq-Gen
sid2nid | Transfer Nucleotide Codes / nids and SNPs / sids
sid2snp | Transfer SNP codes (1, 2, -) and sids (0, 1, 2)
snp2code | Transfer Nucleotide Codes / nids and SNPs / sids
snp2sid | Transfer SNP codes (1, 2, -) and sids (0, 1, 2)
summary.phyclust | Functions for Printing or Summarizing Objects According to Classes

## -- W --

write.fasta | Write Data to Files by Formats
write.fasta.format | Write Data to Files by Formats
write.paml | Write Data to Files by Formats
write.paml.format | Write Data to Files by Formats
write.phylip | Write Data to Files by Formats
write.phylip.format | Write Data to Files by Formats

## -- misc --

.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
.Color | Colors for Identifying Clusters in Plots
.edist.model | Evolution Distance Model
.em.method | EM Methods and Algorithms
.EMC | EM Control
.EMControl | EM Control Generator
.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
.show.option | Show Available Options
.snp | Standard Codes and ids for Nucleotides, SNPs, Codon, Amino Acid and Genetic Code
.substitution.model | Substitution Models for Mutation Processes