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 |
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 |
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. |
plotstruct |
Struct plots of observations based on posterior probabilities |
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.missing |
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.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 |