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phyclust

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  • Author: Wei-Chen Chen and Karin Dorman

Phylogenetic clustering (phyloclustering) is an evolutionary Continuous Time Markov Chain model-based approach to identify population structure from molecular data without assuming linkage equilibrium. The package phyclust (Chen 2011) provides a convenient implementation of phyloclustering for DNA and SNP data, capable of clustering individuals into subpopulations and identifying molecular sequences representative of those subpopulations. It is designed in C for performance, interfaced with R for visualization, and incorporates other popular open source programs including ms (Hudson 2002), seq-gen (Rambaut and Grassly 1997), Hap-Clustering (Tzeng 2005) and PAML baseml (Yang 1997, 2007), for simulating data, additional analyses, and searching the best tree. See the phyclust website for more information, documentations and examples.

Installation

phyclust requires

  • R version 3.0.0 or higher.
  • R package ape.

The package can be installed from the CRAN via the usual install.packages("phyclust"), or via the devtools package:

library(devtools)
install_github("snoweye/phyclust")

Copyright

See phyclust/inst/Documents/ for files in src/msdir/, src/seq-gen/, src/paml_baseml, and R/ttzeng-*.r.

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Version

Install

install.packages('phyclust')

Monthly Downloads

6,682

Version

0.1-25

License

GPL (>= 2)

Maintainer

Wei-Chen Chen

Last Published

August 25th, 2019

Functions in phyclust (0.1-25)

.em.method

EM Methods and Algorithms
phyclust-package

Phyloclustering -- Phylogenetic Clustering
.EMC

EM Control
.identifier

Identifiers for Evolution Models
.EMControl

EM Control Generator
.boundary.method

Boundary Methods for Population Proportions
.init.method

Initialization Methods for EM Algorithms
.Color

Colors for Identifying Clusters in Plots
.edist.model

Evolution Distance Model
.code.type

Code Types of Dataset and Substitution Models
standard.code

Standard Codes and ids for Nucleotides, SNPs, Codon, Amino Acid and Genetic Code
data.phylip.pony

Great Pony 524 EIAV rev Dataset in the phylip Format
.substitution.model

Substitution Models for Mutation Processes
file.read

Read Data from Files by Formats and Return a seq.data Object
.label.method

Label Method
find.best

Find the Best Solution of phyclust
gen.equal.star.anc.dec

Generate Comprehensive Trees.
.init.procedure

Initialization Procedures for EM Algorithms
find.consensus

Find the Consensus Sequence
file.write

Write Data to Files by Formats
phyclust.se

The Main Function of phyclust for Sequencing Error Models
.se.model

Sequencing Error Model
bootstrap.seq

Bootstrap Sequences from a Fitted Model and Star Tree.
bootstrap.seq.data

Bootstrap a seq.data from a Fitted Model.
phyclust

The Main Function of phyclust
phyclust.edist

Evolution Distance of Sequences
plotgaps

Gaps Plots of Sequences for Visual Comparisons
gen.unit.K

Generate Comprehensive Trees.
plothist

Plot Histogram to Compare Number of Mutations.
phyclust.em.step

One EM-step of phyclust
phyclust.e.step

One E-Step of phyclust
get.rooted.tree.height

Get a Rooted Tree Height
phyclust.se.update

Update phyclust Results by the Sequencing Error Model
as.star.tree

Coerce a Rooted Tree to a Star Tree in Class phylo
phyclust.m.step

One M-Step of phyclust
data.fasta.pony

Great Pony 625 EIAV rev Dataset in the Fasta Format
haplo.post.prob

Tzeng's Method: Haplotype Grouping for SNP Sequences
data.phylip.crohn

Crohn's Disease SNP Dataset in the phylip Format
RRand

Rand Index and Adjusted Rand Index
phyclust.logL

Log-Likelihood of phyclust
phyclust.update

Update phyclust Results
getcut.fun

Tzeng's Method: Finding the Best Number of Clusters
plotdots

Dots Plots of Sequences for Visual Comparisons
bootstrap.star.trees

Bootstrap a Star Tree from a Fitted Model.
code2nid

Transfer Codes (A, G, C, T, -) and nids (0, 1, 2, 3, 4)
.show.option

Show Available Options
code2snp

Transfer Nucleotide Codes / nids and SNPs / sids
plotstruct

Struct Plots of Observations Based on Posterior Probabilities
seqgen

Seq-Gen
seq.data

A Toy Dataset in Class seq.data
plotnj

Plot an Unrooted Trees.
gen.seq

Generate Sequences Given a Rooted Tree.
gen.star.tree

Generate a Rooted Tree with a Star Shape
paml.baseml

Phylogenetic Analysis by Maximum Likelihood for Nucleotide Sequences
ms

Generating Samples under a Wright-Fisher Neutral Model of Genetic Variation
nid.aid.cid

Transfer nids (0, 1, ..., 4) , aids (0, 1, ..., 21) and cids (0, 1, ..., 64)
bootstrap.star.trees.seq

Bootstrap Sequences from a Fitted Model.
read.seqgen

Read seqgen's Results and Return a seq.data
snp2sid

Transfer SNP codes (1, 2, -) and sids (0, 1, 2)
all.internal

All Internal Functions of phyclust
rescale.rooted.tree

Rescale a Rooted Tree's Height
print.object

Functions for Printing or Summarizing Objects According to Classes
all.internal.tzeng

All Internal Functions of Tzeng's Methods
phyclust.Pt

Transition Probabilities of phyclust Given Time
prune.Mu

Prune the Center Sequences Mu