| 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 |
| 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 |
| 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 |
| 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 |
| .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 |