Files in snoweye/phyclust

Phylogenetic Clustering (Phyloclustering)

COPYING

ChangeLog

DESCRIPTION

NAMESPACE

R/000_globalVariables.r R/b_seq.r R/b_star_tree.r R/f_base.r R/f_control.r R/f_file.r R/f_file_fasta.r R/f_file_paml.r R/f_file_phylip.r R/f_file_seqgen.r R/f_find_best.r R/f_find_consensus.r R/f_mytool.r R/f_phyclust.r R/f_phyclust_Pt.r R/f_phyclust_edist.r R/f_phyclust_em_step.r R/f_phyclust_logL.r R/f_phyclust_se.r R/f_phyclust_se_update.r R/f_phyclust_update.r R/f_plotdots.r R/f_plotfd.r R/f_plotgaps.r R/f_plothist.r R/f_plotnj.r R/f_plotstruct.r R/f_prune_mu.r R/f_show_option.r R/f_summary.r R/fcn_RRand.r R/p_ms.r R/p_paml_baseml.r R/p_seqgen.r R/p_tool_seq.r R/p_tool_star_tree.r R/tzeng-code.getPIstar.getBigMatB.r R/tzeng-functions.r R/tzeng-main.functions.forRDscoreTest.public.r R/tzeng-modified.r R/zzz.r README.md

cleanup

data/EMC.rda

data/color.r data/control.r

data/crohn.phy

data/pony524.phy

data/pony625.fas

data/seq.data.gap.rda

data/seq.data.toy.rda

data/stdcode.rda

demo/00Index

demo/em_step.r demo/ex_trees.r demo/pony_524.r demo/simu_ms.r demo/simu_ms_tbs.r demo/simu_seqgen_anc.r demo/simu_seqgen_anc_SNP.r demo/toy.r demo/toy_missing.r demo/toy_paml_baseml.r demo/tzeng2005.r

inst/CITATION

inst/Documents/00_Readme-ms.txt

inst/Documents/00_Readme-paml_baseml.txt

inst/Documents/00_Readme-phyclust-c.txt

inst/Documents/00_Readme-seq-gen.txt

inst/Documents/ms-Readme.txt

inst/Documents/paml_baseml-Readme.txt

inst/Documents/seq-gen-Readme.txt

inst/Documents/tzeng-Readme.txt

inst/doc/index_doc.html

inst/doc/phyclust-guide.Rnw

inst/doc/phyclust-guide.pdf inst/test/test.r man/00_phyclust-package.Rd man/11_d.Color.Rd man/11_d.EMC.Rd man/11_d.EMControl.Rd man/11_d.boundary.method.Rd man/11_d.code.type.Rd man/11_d.edist.model.Rd man/11_d.em.method.Rd man/11_d.identifier.Rd man/11_d.init.method.Rd man/11_d.init.procedure.Rd man/11_d.label.method.Rd man/11_d.se.model.Rd man/11_d.show.option.Rd man/11_d.standard.code.Rd man/11_d.substitution.Rd man/RRand.Rd man/as.star.tree.Rd man/bootstrap.seq.Rd man/bootstrap.seq.data.Rd man/bootstrap.star.trees.Rd man/bootstrap.star.trees.seq.Rd man/code2nid.Rd man/code2snp.Rd man/data.fasta.pony.Rd man/data.phylip.crohn.Rd man/data.phylip.pony.Rd man/file.read.Rd man/file.write.Rd man/find.best.Rd man/find.consensus.Rd man/gen.equal.star.anc.dec.Rd man/gen.seq.Rd man/gen.star.tree.Rd man/gen.unit.K.Rd man/get.rooted.tree.height.Rd man/getcut.fun.Rd man/haplo.post.prob.Rd man/ms.Rd man/nid.aid.cid.Rd man/paml.baseml.Rd man/phyclust.Pt.Rd man/phyclust.Rd man/phyclust.e.step.Rd man/phyclust.edist.Rd man/phyclust.em.step.Rd man/phyclust.logL.Rd man/phyclust.m.step.Rd man/phyclust.se.Rd man/phyclust.se.update.Rd man/phyclust.update.Rd man/plotdots.Rd man/plotgaps.Rd man/plothist.Rd man/plotnj.Rd man/plotstruct.Rd man/print.summary.Rd man/prune.Mu.Rd man/read.seqgen.Rd man/rescale.rooted.tree.Rd man/seq.data.Rd man/seqgen.Rd man/snp2sid.Rd man/zz_all.internal.Rd man/zz_all.internal.tzeng.Rd

src/Makevars

src/RRand.c

src/R_RRand.c

src/R_phyclust.c

src/R_phyclust.h

src/R_phyclust_edist.c

src/R_phyclust_em_step.c

src/R_phyclust_find_consensus.c

src/R_phyclust_label.c

src/R_phyclust_logL.c

src/R_phyclust_logPt.c

src/R_phyclust_qmatrix.c

src/R_phyclust_se.c

src/R_phyclust_se.h

src/R_phyclust_se_update.c

src/R_phyclust_struct.c

src/R_phyclust_update.c

src/make/inc.msdir

src/make/inc.paml_baseml

src/make/inc.phyclust

src/make/inc.seq-gen

src/make/inc.src

src/msdir/R_ms.h

src/msdir/R_ms_main.c

src/msdir/R_rand.c

src/msdir/ms.c

src/msdir/ms.h

src/msdir/ms_main.c

src/msdir/streec.c

src/paml_baseml/R_paml.h

src/paml_baseml/R_paml_baseml_main.c

src/paml_baseml/baseml.c

src/paml_baseml/paml.h

src/paml_baseml/tools.c

src/paml_baseml/treespace.c

src/paml_baseml/treesub.c

src/phyclust/phyclust.h

src/phyclust/phyclust_ape_nj.c

src/phyclust/phyclust_ape_nj.h

src/phyclust/phyclust_constant.h

src/phyclust/phyclust_edist.c

src/phyclust/phyclust_edist.h

src/phyclust/phyclust_em.h

src/phyclust/phyclust_em_control.c

src/phyclust/phyclust_em_fp.c

src/phyclust/phyclust_em_phyclust_struct.c

src/phyclust/phyclust_em_step.c

src/phyclust/phyclust_em_tool.c

src/phyclust/phyclust_em_tool.h

src/phyclust/phyclust_file_input.c

src/phyclust/phyclust_file_input.h

src/phyclust/phyclust_init_method.c

src/phyclust/phyclust_init_method.h

src/phyclust/phyclust_init_method_ex.c

src/phyclust/phyclust_init_method_kmed.c

src/phyclust/phyclust_init_method_nj.c

src/phyclust/phyclust_init_method_pam.c

src/phyclust/phyclust_init_procedure.c

src/phyclust/phyclust_init_procedure.h

src/phyclust/phyclust_label.c

src/phyclust/phyclust_label.h

src/phyclust/phyclust_logpL.c

src/phyclust/phyclust_logpL.h

src/phyclust/phyclust_optim_nmmin.c

src/phyclust/phyclust_optim_nmmin.h

src/phyclust/phyclust_pam.c

src/phyclust/phyclust_pam_ind_2.h

src/phyclust/phyclust_qmatrix.c

src/phyclust/phyclust_qmatrix.h

src/phyclust/phyclust_qmatrix_array.c

src/phyclust/phyclust_qmatrix_array.h

src/phyclust/phyclust_se_convolution_em_step.c

src/phyclust/phyclust_se_convolution_em_tool.c

src/phyclust/phyclust_se_convolution_logpL.c

src/phyclust/phyclust_se_convolution_logpL.h

src/phyclust/phyclust_se_em.h

src/phyclust/phyclust_se_em_fp.c

src/phyclust/phyclust_se_em_phyclust_struct.c

src/phyclust/phyclust_se_em_tool.c

src/phyclust/phyclust_se_pmatrix.c

src/phyclust/phyclust_se_pmatrix.h

src/phyclust/phyclust_se_struct.c

src/phyclust/phyclust_se_struct.h

src/phyclust/phyclust_struct.c

src/phyclust/phyclust_struct.h

src/phyclust/phyclust_tool.c

src/phyclust/phyclust_tool.h

src/seq-gen/R_seq-gen.h

src/seq-gen/R_seq-gen_main.c

src/seq-gen/aamodels.c

src/seq-gen/aamodels.h

src/seq-gen/eigen.c

src/seq-gen/eigen.h

src/seq-gen/evolve.c

src/seq-gen/evolve.h

src/seq-gen/gamma.c

src/seq-gen/gamma.h

src/seq-gen/global.c

src/seq-gen/global.h

src/seq-gen/model.c

src/seq-gen/model.h

src/seq-gen/nucmodels.c

src/seq-gen/nucmodels.h

src/seq-gen/seq-gen.c

src/seq-gen/tree.h

src/seq-gen/treefile.c

src/seq-gen/treefile.h

src/seq-gen/twister.c

src/seq-gen/twister.h

src/zzz.c

src/zzz.h

vignettes/build_pdf.sh

vignettes/index_doc.html

vignettes/phyclust-guide.Rnw

vignettes/phyclust-include/01-introduction.tex

vignettes/phyclust-include/02-dataio.tex

vignettes/phyclust-include/03-msseqgen.tex

vignettes/phyclust-include/04-phyclust.tex

vignettes/phyclust-include/05-paml_baseml.tex

vignettes/phyclust-include/06-haplo.tex

vignettes/phyclust-include/f-getcut.pdf vignettes/phyclust-include/f-ms.pdf vignettes/phyclust-include/f-paml_baseml.pdf vignettes/phyclust-include/f-super.pdf vignettes/phyclust-include/f-toydots.pdf vignettes/phyclust-include/f-toyhist.pdf vignettes/phyclust-include/f-toynj.pdf

vignettes/phyclust-include/my_jss.cls

vignettes/phyclust-include/phyclust.bib

snoweye/phyclust documentation built on Sept. 12, 2023, 5 a.m.