A B C D F G H M N P R S W misc
phyclust-package | Phyloclustering - Phylogenetic Clustering |
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 |
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. |
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 |
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 |
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 |
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 |
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) |
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 |
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 |
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 |
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 |
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 |
.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 |