phyclust: 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.

AuthorWei-Chen Chen [aut, cre], Karin Dorman [aut]
Date of publication2016-12-11 12:26:36
MaintainerWei-Chen Chen <wccsnow@gmail.com>
LicenseGPL (>= 2)
Version0.1-18
http://snoweye.github.io/phyclust/

View on CRAN

Man pages

00_phyclust-package: Phyloclustering - Phylogenetic Clustering

11_d.boundary.method: Boundary Methods for Population Proportions

11_d.code.type: Code Types of Dataset and Substitution Models

11_d.Color: Colors for Identifying Clusters in Plots

11_d.edist.model: Evolution Distance Model

11_d.EMC: EM Control

11_d.EMControl: EM Control Generator

11_d.em.method: EM Methods and Algorithms

11_d.identifier: Identifiers for Evolution Models

11_d.init.method: Initialization Methods for EM Algorithms

11_d.init.procedure: Initialization Procedures for EM Algorithms

11_d.label.method: Label Method

11_d.se.model: Sequencing Error Model

11_d.show.option: Show Available Options

11_d.standard.code: Standard Codes and ids for Nucleotides, SNPs, Codon, Amino...

11_d.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.

code2nid: Transfer Codes (A, G, C, T, -) and nids (0, 1, 2, 3, 4)

code2snp: Transfer Nucleotide Codes / nids and SNPs / sids

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

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

file.write: Write Data to Files by Formats

find.best: Find the Best Solution of phyclust

find.consensus: Find the Consensus Sequence

gen.equal.star.anc.dec: Generate Comprehensive Trees.

gen.seq: Generate Sequences Given a Rooted Tree.

gen.star.tree: Generate a Rooted Tree with a Star Shape

gen.unit.K: Generate Comprehensive Trees.

getcut.fun: Tzeng's Method: Finding the Best Number of Clusters

get.rooted.tree.height: Get a Rooted Tree Height

haplo.post.prob: Tzeng's Method: Haplotype Grouping for SNP Sequences

ms: Generating Samples under a Wright-Fisher Neutral Model of...

nid.aid.cid: Transfer nids (0, 1, ..., 4) , aids (0, 1, ..., 21) and cids...

paml.baseml: Phylogenetic Analysis by Maximum Likelihood for Nucleotide...

phyclust: The Main Function of phyclust

phyclust.edist: Evolution Distance of Sequences

phyclust.em.step: One EM-step of phyclust

phyclust.e.step: One E-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.summary: Functions for Printing or Summarizing Objects According to...

prune.Mu: Prune the Center Sequences Mu

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: A Toy Dataset in Class seq.data

seqgen: Seq-Gen

snp2sid: Transfer SNP codes (1, 2, -) and sids (0, 1, 2)

zz_all.internal: All Internal Functions of phyclust

zz_all.internal.tzeng: All Internal Functions of Tzeng's Methods

Functions

acode2aid Man page
acode2aid.default Man page
acode2aid.list Man page
aid2acode Man page
aid2acode.default Man page
aid2acode.list Man page
.amino.acid Man page
as.star.tree Man page
bootstrap.merge.seq Man page
bootstrap.seq Man page
bootstrap.seq.data Man page
bootstrap.seq.nucleotide Man page
bootstrap.seq.snp Man page
bootstrap.star.tree Man page
bootstrap.star.trees Man page
bootstrap.star.trees.seq Man page
.boundary.method Man page
check.EMC Man page
check.label Man page
chkdim.Add.fun Man page
chkdim.Multiply.fun Man page
cid2aid Man page
cid2aid.default Man page
cid2aid.list Man page
Class baseml Man page
Class ms Man page
Class phyclust Man page
Class phylo Man page
Class seq.data Man page
Class seqgen Man page
code2nid Man page
code2nid.default Man page
code2nid.list Man page
code2snp Man page
code2snp.default Man page
code2snp.list Man page
.code.type Man page
.codon Man page
.Color Man page
construct.bigB.dPI Man page
construct.dB.list.fun Man page
convert.QA.to.vect Man page
Data Crohn's Disease Man page
Data Pony 524 Man page
Data Pony 625 Man page
Data Toy Man page
.edist.model Man page
.EMC Man page
.EMControl Man page
.em.method Man page
final.BigMatB.fun Man page
final.BigMatB.matC.fun Man page
find.best Man page
find.consensus Man page
Format fasta Man page
Format phylip Man page
gen.equal.star.anc.dec Man page
.genetic.code Man page
gen.seq.HKY Man page
gen.seq.SNP Man page
gen.star.tree Man page
gen.unit.K Man page
get.allpossROUTE.fun Man page
get.BB.fun Man page
getBigMatB.fun Man page
getcut.fun Man page
get.deriBigMatB.fun Man page
get.fullBB.fun Man page
getI13.fun Man page
get.I.fun Man page
get.ini.possHap.hapReserv.fun Man page
get.medBB.skip.fun Man page
getPIstar.fun Man page
get.preBB.skip.fun Man page
get.rooted.tree.height Man page
get.step.mut.fun Man page
get.subPI.fun Man page
haplo.phase.known Man page
haplo.post.prob Man page
I33Inv.fun Man page
.identifier Man page
index.k.fun Man page
.init.method Man page
.init.procedure Man page
.label.method Man page
.missing.code Man page
ms Man page
my.cat Man page
my.format Man page
my.print Man page
nid2aid Man page
nid2aid.default Man page
nid2aid.list Man page
nid2cid Man page
nid2cid.default Man page
nid2cid.list Man page
nid2code Man page
nid2code.default Man page
nid2code.list Man page
nid2sid Man page
.nucleotide Man page
paml.baseml Man page
paml.baseml.control Man page
paml.baseml.show.default Man page
phyclust Man page
phyclust.edist Man page
phyclust.em.step Man page
phyclust.e.step Man page
phyclust.logL Man page
phyclust.m.step Man page
phyclust-package Man page
phyclust.Pt Man page
phyclust.se Man page
phyclust.se.update Man page
phyclust.update Man page
plotdots Man page
plotfd Man page
plotgaps Man page
plothist Man page
plothist.my Man page
plotnj Man page
plotstruct Man page
print.baseml Man page
print.ms Man page
print.phyclust Man page
print.Pt Man page
print.RRand Man page
print.seq.data Man page
print.seqgen Man page
prune.Mu Man page
read.fasta Man page
read.fasta.format Man page
read.phylip Man page
read.phylip.format Man page
read.seqgen Man page
rescale.rooted.tree Man page
RRand Man page
.se.model Man page
seq.data.gap Man page
seq.data.toy Man page
seqgen Man page
.show.option Man page
sid2nid Man page
sid2snp Man page
sid2snp.default Man page
sid2snp.list Man page
.snp Man page
snp2code Man page
snp2code.default Man page
snp2code.list Man page
snp2sid Man page
snp2sid.default Man page
snp2sid.list Man page
.substitution.model Man page
summary.phyclust Man page
translate.EMC Man page
translate.EMC.se Man page
translate.ret Man page
translate.ret.se Man page
.tzengEnv Man page
unstrsplit Man page
write.fasta Man page
write.fasta.format Man page
write.paml Man page
write.paml.format Man page
write.phylip Man page
write.phylip.format Man page
zero.mat.fun Man page

Files

phyclust
phyclust/COPYING
phyclust/inst
phyclust/inst/CITATION
phyclust/inst/Documents
phyclust/inst/Documents/ms-Readme.txt
phyclust/inst/Documents/00_Readme-paml_baseml.txt
phyclust/inst/Documents/00_Readme-seq-gen.txt
phyclust/inst/Documents/00_Readme-phyclust-c.txt
phyclust/inst/Documents/tzeng-Readme.txt
phyclust/inst/Documents/seq-gen-Readme.txt
phyclust/inst/Documents/paml_baseml-Readme.txt
phyclust/inst/Documents/00_Readme-ms.txt
phyclust/inst/test
phyclust/inst/test/test.r
phyclust/inst/doc
phyclust/inst/doc/index_doc.html
phyclust/inst/doc/phyclust-guide.pdf
phyclust/inst/doc/phyclust-guide.Rnw
phyclust/src
phyclust/src/R_phyclust.h
phyclust/src/R_phyclust_logL.c
phyclust/src/Makevars
phyclust/src/make
phyclust/src/make/inc.phyclust
phyclust/src/make/inc.msdir
phyclust/src/make/inc.paml_baseml
phyclust/src/make/inc.seq-gen
phyclust/src/make/inc.src
phyclust/src/RRand.c
phyclust/src/R_phyclust_se_update.c
phyclust/src/R_phyclust_update.c
phyclust/src/phyclust
phyclust/src/phyclust/phyclust_se_convolution_logpL.c
phyclust/src/phyclust/phyclust_tool.c
phyclust/src/phyclust/phyclust_se_convolution_logpL.h
phyclust/src/phyclust/phyclust_qmatrix.c
phyclust/src/phyclust/phyclust_logpL.h
phyclust/src/phyclust/phyclust_struct.h
phyclust/src/phyclust/phyclust_em_phyclust_struct.c
phyclust/src/phyclust/phyclust_pam_ind_2.h
phyclust/src/phyclust/phyclust_init_method_pam.c
phyclust/src/phyclust/phyclust_em_tool.h
phyclust/src/phyclust/phyclust_tool.h
phyclust/src/phyclust/phyclust_init_method_ex.c
phyclust/src/phyclust/phyclust_em_step.c
phyclust/src/phyclust/phyclust_optim_nmmin.h
phyclust/src/phyclust/phyclust_se_convolution_em_tool.c
phyclust/src/phyclust/phyclust_qmatrix.h
phyclust/src/phyclust/phyclust_optim_nmmin.c
phyclust/src/phyclust/phyclust_init_method.c
phyclust/src/phyclust/phyclust_pam.c
phyclust/src/phyclust/phyclust_se_pmatrix.h
phyclust/src/phyclust/phyclust_ape_nj.c
phyclust/src/phyclust/phyclust_qmatrix_array.c
phyclust/src/phyclust/phyclust_se_em.h
phyclust/src/phyclust/phyclust_init_procedure.c
phyclust/src/phyclust/phyclust_ape_nj.h
phyclust/src/phyclust/phyclust_struct.c
phyclust/src/phyclust/phyclust_se_em_tool.c
phyclust/src/phyclust/phyclust_se_struct.h
phyclust/src/phyclust/phyclust_em_tool.c
phyclust/src/phyclust/phyclust_se_em_fp.c
phyclust/src/phyclust/phyclust_se_convolution_em_step.c
phyclust/src/phyclust/phyclust_edist.h
phyclust/src/phyclust/phyclust_se_em_phyclust_struct.c
phyclust/src/phyclust/phyclust_init_method.h
phyclust/src/phyclust/phyclust_label.h
phyclust/src/phyclust/phyclust_file_input.h
phyclust/src/phyclust/phyclust_em.h
phyclust/src/phyclust/phyclust_em_fp.c
phyclust/src/phyclust/phyclust_init_procedure.h
phyclust/src/phyclust/phyclust_se_pmatrix.c
phyclust/src/phyclust/phyclust_init_method_kmed.c
phyclust/src/phyclust/phyclust_se_struct.c
phyclust/src/phyclust/phyclust_file_input.c
phyclust/src/phyclust/phyclust_qmatrix_array.h
phyclust/src/phyclust/phyclust_logpL.c
phyclust/src/phyclust/phyclust_constant.h
phyclust/src/phyclust/phyclust_label.c
phyclust/src/phyclust/phyclust_em_control.c
phyclust/src/phyclust/phyclust_edist.c
phyclust/src/phyclust/phyclust.h
phyclust/src/phyclust/phyclust_init_method_nj.c
phyclust/src/R_phyclust_label.c
phyclust/src/R_phyclust_qmatrix.c
phyclust/src/R_phyclust.c
phyclust/src/R_phyclust_edist.c
phyclust/src/R_phyclust_struct.c
phyclust/src/R_phyclust_se.h
phyclust/src/seq-gen
phyclust/src/seq-gen/nucmodels.h
phyclust/src/seq-gen/twister.h
phyclust/src/seq-gen/gamma.c
phyclust/src/seq-gen/aamodels.c
phyclust/src/seq-gen/eigen.h
phyclust/src/seq-gen/evolve.c
phyclust/src/seq-gen/nucmodels.c
phyclust/src/seq-gen/evolve.h
phyclust/src/seq-gen/global.c
phyclust/src/seq-gen/aamodels.h
phyclust/src/seq-gen/tree.h
phyclust/src/seq-gen/model.h
phyclust/src/seq-gen/eigen.c
phyclust/src/seq-gen/R_seq-gen.h
phyclust/src/seq-gen/model.c
phyclust/src/seq-gen/global.h
phyclust/src/seq-gen/R_seq-gen_main.c
phyclust/src/seq-gen/treefile.h
phyclust/src/seq-gen/twister.c
phyclust/src/seq-gen/gamma.h
phyclust/src/seq-gen/treefile.c
phyclust/src/seq-gen/seq-gen.c
phyclust/src/R_phyclust_find_consensus.c
phyclust/src/R_phyclust_se.c
phyclust/src/paml_baseml
phyclust/src/paml_baseml/treespace.c
phyclust/src/paml_baseml/paml.h
phyclust/src/paml_baseml/treesub.c
phyclust/src/paml_baseml/R_paml_baseml_main.c
phyclust/src/paml_baseml/R_paml.h
phyclust/src/paml_baseml/tools.c
phyclust/src/paml_baseml/baseml.c
phyclust/src/R_RRand.c
phyclust/src/R_phyclust_logPt.c
phyclust/src/R_phyclust_em_step.c
phyclust/src/msdir
phyclust/src/msdir/R_rand.c
phyclust/src/msdir/ms_main.c
phyclust/src/msdir/ms.c
phyclust/src/msdir/ms.h
phyclust/src/msdir/R_ms.h
phyclust/src/msdir/streec.c
phyclust/src/msdir/R_ms_main.c
phyclust/NAMESPACE
phyclust/demo
phyclust/demo/toy_missing.r
phyclust/demo/pony_524.r
phyclust/demo/simu_ms.r
phyclust/demo/em_step.r
phyclust/demo/ex_trees.r
phyclust/demo/tzeng2005.r
phyclust/demo/00Index
phyclust/demo/simu_seqgen_anc_SNP.r
phyclust/demo/toy_paml_baseml.r
phyclust/demo/simu_ms_tbs.r
phyclust/demo/toy.r
phyclust/demo/simu_seqgen_anc.r
phyclust/data
phyclust/data/crohn.phy
phyclust/data/control.r
phyclust/data/EMC.rda
phyclust/data/stdcode.rda
phyclust/data/color.r
phyclust/data/seq.data.toy.rda
phyclust/data/pony625.fas
phyclust/data/seq.data.gap.rda
phyclust/data/pony524.phy
phyclust/R
phyclust/R/f_plothist.r
phyclust/R/tzeng-modified.r
phyclust/R/f_plotdots.r
phyclust/R/f_find_best.r
phyclust/R/000_globalVariables.r
phyclust/R/tzeng-functions.r
phyclust/R/f_plotfd.r
phyclust/R/f_base.r
phyclust/R/tzeng-code.getPIstar.getBigMatB.r
phyclust/R/f_phyclust_se.r
phyclust/R/f_summary.r
phyclust/R/b_seq.r
phyclust/R/b_star_tree.r
phyclust/R/f_plotgaps.r
phyclust/R/p_seqgen.r
phyclust/R/f_phyclust_se_update.r
phyclust/R/p_tool_seq.r
phyclust/R/f_file_paml.r
phyclust/R/f_phyclust_edist.r
phyclust/R/p_tool_star_tree.r
phyclust/R/f_phyclust_Pt.r
phyclust/R/tzeng-main.functions.forRDscoreTest.public.r
phyclust/R/f_control.r
phyclust/R/f_file_seqgen.r
phyclust/R/f_file_fasta.r
phyclust/R/f_phyclust_update.r
phyclust/R/f_show_option.r
phyclust/R/f_file_phylip.r
phyclust/R/f_find_consensus.r
phyclust/R/zzz.r
phyclust/R/f_file.r
phyclust/R/f_phyclust_logL.r
phyclust/R/p_paml_baseml.r
phyclust/R/f_phyclust.r
phyclust/R/f_prune_mu.r
phyclust/R/p_ms.r
phyclust/R/f_phyclust_em_step.r
phyclust/R/f_mytool.r
phyclust/R/f_plotstruct.r
phyclust/R/f_plotnj.r
phyclust/R/fcn_RRand.r
phyclust/vignettes
phyclust/vignettes/index_doc.html
phyclust/vignettes/phyclust-guide.Rnw
phyclust/vignettes/phyclust-include
phyclust/vignettes/phyclust-include/f-super.pdf
phyclust/vignettes/phyclust-include/f-toydots.pdf
phyclust/vignettes/phyclust-include/03-msseqgen.tex
phyclust/vignettes/phyclust-include/04-phyclust.tex
phyclust/vignettes/phyclust-include/f-paml_baseml.pdf
phyclust/vignettes/phyclust-include/06-haplo.tex
phyclust/vignettes/phyclust-include/f-ms.pdf
phyclust/vignettes/phyclust-include/f-toynj.pdf
phyclust/vignettes/phyclust-include/01-introduction.tex
phyclust/vignettes/phyclust-include/my_jss.cls
phyclust/vignettes/phyclust-include/02-dataio.tex
phyclust/vignettes/phyclust-include/phyclust.bib
phyclust/vignettes/phyclust-include/05-paml_baseml.tex
phyclust/vignettes/phyclust-include/f-getcut.pdf
phyclust/vignettes/phyclust-include/f-toyhist.pdf
phyclust/vignettes/build_pdf.sh
phyclust/README.md
phyclust/MD5
phyclust/DESCRIPTION
phyclust/ChangeLog
phyclust/man
phyclust/man/nid.aid.cid.Rd phyclust/man/phyclust.Pt.Rd phyclust/man/getcut.fun.Rd phyclust/man/phyclust.se.Rd phyclust/man/phyclust.em.step.Rd phyclust/man/seqgen.Rd phyclust/man/RRand.Rd phyclust/man/code2nid.Rd phyclust/man/11_d.code.type.Rd phyclust/man/print.summary.Rd phyclust/man/file.read.Rd phyclust/man/11_d.se.model.Rd phyclust/man/data.phylip.crohn.Rd phyclust/man/gen.unit.K.Rd phyclust/man/gen.equal.star.anc.dec.Rd phyclust/man/00_phyclust-package.Rd phyclust/man/plotgaps.Rd phyclust/man/11_d.Color.Rd phyclust/man/bootstrap.star.trees.seq.Rd phyclust/man/phyclust.edist.Rd phyclust/man/code2snp.Rd phyclust/man/11_d.init.procedure.Rd phyclust/man/plotstruct.Rd phyclust/man/file.write.Rd phyclust/man/11_d.identifier.Rd phyclust/man/phyclust.Rd phyclust/man/data.phylip.pony.Rd phyclust/man/phyclust.se.update.Rd phyclust/man/plotdots.Rd phyclust/man/11_d.EMC.Rd phyclust/man/find.consensus.Rd phyclust/man/snp2sid.Rd phyclust/man/read.seqgen.Rd phyclust/man/get.rooted.tree.height.Rd phyclust/man/phyclust.m.step.Rd phyclust/man/bootstrap.seq.data.Rd phyclust/man/phyclust.e.step.Rd phyclust/man/data.fasta.pony.Rd phyclust/man/find.best.Rd phyclust/man/paml.baseml.Rd phyclust/man/plothist.Rd phyclust/man/gen.seq.Rd phyclust/man/rescale.rooted.tree.Rd phyclust/man/11_d.substitution.Rd phyclust/man/zz_all.internal.Rd phyclust/man/haplo.post.prob.Rd phyclust/man/ms.Rd phyclust/man/11_d.init.method.Rd phyclust/man/phyclust.update.Rd phyclust/man/plotnj.Rd phyclust/man/zz_all.internal.tzeng.Rd phyclust/man/gen.star.tree.Rd phyclust/man/11_d.em.method.Rd phyclust/man/phyclust.logL.Rd phyclust/man/bootstrap.star.trees.Rd phyclust/man/11_d.label.method.Rd phyclust/man/as.star.tree.Rd phyclust/man/11_d.standard.code.Rd phyclust/man/seq.data.Rd phyclust/man/prune.Mu.Rd phyclust/man/11_d.EMControl.Rd phyclust/man/bootstrap.seq.Rd phyclust/man/11_d.show.option.Rd phyclust/man/11_d.boundary.method.Rd phyclust/man/11_d.edist.model.Rd
phyclust/cleanup

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