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| phyclust-package | Phyloclustering - Phylogenetic Clustering |
| .boundary.method | Boundary methods for population proportions |
| .code.type | Code types of dataset and substitution models |
| .Color | Colors for identifying clusters in plots |
| .edist.model | Evolution distance model |
| .em.method | EM methods/algorithms |
| .EMC | EM control |
| .EMControl | EM control generator |
| .identifier | Identifiers for evolution models |
| .init.method | Initialization methods for EM algorithms |
| .init.procedure | Initialization procedures for EM algorithms |
| .nucleotide | Standard codes and ids for nucleotides and SNPs |
| .show.option | Show available options |
| .snp | Standard codes and ids for nucleotides and SNPs |
| .substitution | Substitution models for mutation processes |
| 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. |
| 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 |
| 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 |
| nid2code | Transfer codes (A, G, C, T, -) and nids (0, 1, 2, 3, 4) |
| nid2sid | Transfer nucleotide codes / nids and SNPs / sids |
| 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 |
| plotdots | Dots plots of sequences for visual comparisons |
| plothist | Plot histogram to compare number of mutations. |
| plotnj | Plot an unrooted trees. |
| 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 |
| read.fasta | Read data from files by formats and return a seq.data |
| read.fasta.nucleotide | Read data from files by formats and return a seq.data |
| read.phylip | Read data from files by formats and return a seq.data |
| read.phylip.nucleotide | Read data from files by formats and return a seq.data |
| read.phylip.snp | Read data from files by formats and return a seq.data |
| 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.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.nucleotide | Write data to files by formats |
| write.phylip | Write data to files by formats |
| write.phylip.nucleotide | Write data to files by formats |
| write.phylip.snp | Write data to files by formats |