Phylogenetic Clustering (Phyloclustering)

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Documentation for package ‘phyclust’ version 0.1-34

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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