phyclust: Phylogenetic Clustering (Phyloclustering)

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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.

Author
Wei-Chen Chen [aut, cre], Karin Dorman [aut]
Date of publication
2016-07-15 10:14:34
Maintainer
Wei-Chen Chen <wccsnow@gmail.com>
License
GPL (>= 2)
Version
0.1-17
URLs

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