phyclust v0.1-24

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Phylogenetic Clustering (Phyloclustering)

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) <doi:10.1093/bioinformatics/18.2.337>, seq-gen (Rambaut and Grassly 1997) <doi:10.1093/bioinformatics/13.3.235>, Hap-Clustering (Tzeng 2005) <doi:10.1002/gepi.20063> and PAML baseml (Yang 1997, 2007) <doi:10.1093/bioinformatics/13.5.555>, <doi:10.1093/molbev/msm088>, for simulating data, additional analyses, and searching the best tree. See the phyclust website for more information, documentations and examples.

Readme

phyclust

  • License: License
  • Download: Download
  • 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")

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

Functions in phyclust

Name Description
.identifier Identifiers for Evolution Models
.boundary.method Boundary Methods for Population Proportions
.code.type Code Types of Dataset and Substitution Models
file.write Write Data to Files by Formats
.EMC EM Control
data.fasta.pony Great Pony 625 EIAV rev Dataset in the Fasta Format
data.phylip.crohn Crohn's Disease SNP Dataset in the phylip Format
.init.method Initialization Methods for EM Algorithms
standard.code Standard Codes and ids for Nucleotides, SNPs, Codon, Amino Acid and Genetic Code
.substitution.model Substitution Models for Mutation Processes
getcut.fun Tzeng's Method: Finding the Best Number of Clusters
RRand Rand Index and Adjusted Rand Index
.EMControl EM Control Generator
as.star.tree Coerce a Rooted Tree to a Star Tree in Class phylo
find.best Find the Best Solution of phyclust
.se.model Sequencing Error Model
.show.option Show Available Options
haplo.post.prob Tzeng's Method: Haplotype Grouping for SNP Sequences
data.phylip.pony Great Pony 524 EIAV rev Dataset in the phylip Format
file.read Read Data from Files by Formats and Return a seq.data Object
find.consensus Find the Consensus Sequence
phyclust.edist Evolution Distance of Sequences
gen.unit.K Generate Comprehensive Trees.
gen.equal.star.anc.dec Generate Comprehensive Trees.
.edist.model Evolution Distance Model
gen.seq Generate Sequences Given a Rooted Tree.
get.rooted.tree.height Get a Rooted Tree Height
.em.method EM Methods and Algorithms
bootstrap.seq Bootstrap Sequences from a Fitted Model and Star Tree.
bootstrap.seq.data Bootstrap a seq.data from a Fitted Model.
phyclust.logL Log-Likelihood of phyclust
phyclust.se The Main Function of phyclust for Sequencing Error Models
phyclust.se.update Update phyclust Results by the Sequencing Error Model
code2nid Transfer Codes (A, G, C, T, -) and nids (0, 1, 2, 3, 4)
phyclust.em.step One EM-step of phyclust
print.object Functions for Printing or Summarizing Objects According to Classes
phyclust.m.step One M-Step of phyclust
read.seqgen Read seqgen's Results and Return a seq.data
rescale.rooted.tree Rescale a Rooted Tree's Height
plotnj Plot an Unrooted Trees.
gen.star.tree Generate a Rooted Tree with a Star Shape
prune.Mu Prune the Center Sequences Mu
seq.data A Toy Dataset in Class seq.data
seqgen Seq-Gen
code2snp Transfer Nucleotide Codes / nids and SNPs / sids
bootstrap.star.trees Bootstrap a Star Tree from a Fitted Model.
phyclust The Main Function of phyclust
phyclust.e.step One E-Step of phyclust
phyclust.update Update phyclust Results
bootstrap.star.trees.seq Bootstrap Sequences from a Fitted Model.
plotdots Dots Plots of Sequences for Visual Comparisons
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)
plotstruct Struct Plots of Observations Based on Posterior Probabilities
snp2sid Transfer SNP codes (1, 2, -) and sids (0, 1, 2)
paml.baseml Phylogenetic Analysis by Maximum Likelihood for Nucleotide Sequences
all.internal All Internal Functions of phyclust
phyclust.Pt Transition Probabilities of phyclust Given Time
plotgaps Gaps Plots of Sequences for Visual Comparisons
plothist Plot Histogram to Compare Number of Mutations.
all.internal.tzeng All Internal Functions of Tzeng's Methods
.init.procedure Initialization Procedures for EM Algorithms
.label.method Label Method
phyclust-package Phyloclustering -- Phylogenetic Clustering
.Color Colors for Identifying Clusters in Plots
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Vignettes of phyclust

Name
phyclust-include/01-introduction.tex
phyclust-include/02-dataio.tex
phyclust-include/03-msseqgen.tex
phyclust-include/04-phyclust.tex
phyclust-include/05-paml_baseml.tex
phyclust-include/06-haplo.tex
phyclust-include/f-getcut.pdf
phyclust-include/f-ms.pdf
phyclust-include/f-paml_baseml.pdf
phyclust-include/f-super.pdf
phyclust-include/f-toydots.pdf
phyclust-include/f-toyhist.pdf
phyclust-include/f-toynj.pdf
phyclust-include/my_jss.cls
phyclust-include/phyclust.bib
build_pdf.sh
index_doc.html
phyclust-guide.Rnw
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Details

Date 2019-03-20
LazyLoad yes
LazyData yes
Copyright See phyclust/inst/Documents/ for files in src/msdir/, src/seq-gen/, src/paml_baseml, and R/ttzeng-*.r.
BugReports https://github.com/snoweye/phyclust/issues
License GPL (>= 2)
URL http://snoweye.github.io/phyclust/
NeedsCompilation yes
Packaged 2019-03-25 00:23:06 UTC; snoweye
Repository CRAN
Date/Publication 2019-03-27 10:00:03 UTC
depends ape , R (>= 3.0.0)
Contributors Karin Dorman

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