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

Files in this package

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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