Files in rphast
Interface to PHAST Software for Comparative Genomics

inst
inst/examples
inst/examples/summary-tree.R inst/examples/likelihood-msa.R inst/examples/write-wig.R inst/examples/sub-msa.R inst/examples/phastCons.R inst/examples/col-expected-subs-msa.R inst/examples/score-hmm.R inst/examples/as-data-frame-feat.R inst/examples/split-by-feature-msa.R inst/examples/as-pointer-feat.R inst/examples/summary-tm.R inst/examples/read-msa.R inst/examples/subtree.R inst/examples/reflect-phylo-hmm.R inst/examples/convert-coords-feat.R inst/examples/write-msa.R inst/examples/is-subst-mod-tm.R inst/examples/phyloP.R inst/examples/subst-mods.R inst/examples/plot-msa.R inst/examples/hmm.R inst/examples/numnodes-tree.R inst/examples/as-pointer-msa.R inst/examples/nrow-feat.R inst/examples/prune-tree.R inst/examples/offset-msa.R inst/examples/fix-semicolon-tree.R inst/examples/feat.R inst/examples/names-msa.R inst/examples/coverage-feat.R inst/examples/plot-lsmodel-tm.R inst/examples/postprob-msa.R inst/examples/square-bracket-assign-msa.R inst/examples/informative-regions-msa.R inst/examples/fix-start-stop-feat.R inst/examples/expected-subs-msa.R inst/examples/mod-backgd-tm.R inst/examples/write-hmm.R inst/examples/write-wig-feat.R inst/examples/strip-gaps-msa.R inst/examples/add-introns-feat.R inst/examples/get4d-msa.R inst/examples/sample-msa.R inst/examples/phyloP-prior.R inst/examples/square-bracket-msa.R inst/examples/tm.R inst/examples/print-msa.R inst/examples/simulate-msa.R inst/examples/ncol-msa.R inst/examples/label-branches.R inst/examples/translate-msa.R inst/examples/as-track-feat.R inst/examples/read-feat.R inst/examples/add-signals-feat.R inst/examples/nrow-msa.R inst/examples/summary-msa.R inst/examples/is-ordered-msa.R inst/examples/read-hmm.R inst/examples/read-newick-tree.R inst/examples/name-ancestors.R inst/examples/alphabet-msa.R inst/examples/rescale-tree.R inst/examples/dim-feat.R inst/examples/print-tm.R inst/examples/phyloFit.R inst/examples/add-UTRs-feat.R inst/examples/write-feat.R inst/examples/plot-tm.R inst/examples/rename-tree.R inst/examples/msa.R inst/examples/as-list-tm.R inst/examples/plot-feat.R inst/examples/plot-gene.R inst/examples/read-tm.R inst/examples/total-expected-subs-msa.R inst/examples/from-pointer-msa.R inst/examples/overlap-feat.R inst/examples/label-subtree.R inst/examples/summary-feat.R inst/examples/guess-format-msa.R inst/examples/ncol-feat.R inst/examples/write-tm.R inst/examples/tagval.R inst/examples/is-format-msa.R inst/examples/tagval-feat.R
inst/extdata
inst/extdata/NRSF.zip
inst/extdata/examples.zip
inst/doc
inst/doc/vignette1.Rnw
inst/doc/vignette4.Rnw
inst/doc/vignette3.pdf inst/doc/vignette1.R inst/doc/vignette3.R inst/doc/vignette4.pdf inst/doc/vignette4.R inst/doc/vignette1.pdf
inst/doc/vignette3.Rnw
configure.ac
tests
tests/msa.examples.R tests/phyloP.examples.R tests/optim.examples.R tests/feat.examples.R
src
src/queues.h
src/hmm.c
src/tfbs.c
src/phylo_p_print.h
src/hashtable.h
src/prob_vector.h
src/phylo_p.h
src/simplex_grid.h
src/bed.h
src/matrix.c
src/bed.c
src/maf.c
src/hashtable.c
src/rph_category_map.c
src/list_of_lists.c
src/indel_mod.h
src/em.h
src/fit_column.h
src/phylo_hmm.c
src/sufficient_stats.c
src/tree_model.c
src/gap_patterns.c
src/rph_phastCons.c
src/fit_column.c
src/rph_hmm.c
src/subst_distrib.c
src/stacks.h
src/pbs_code.h
src/list_of_lists.h
src/subst_mods.h
src/misc.c
src/sufficient_stats.h
src/rph_trees.c
src/complex_vector.h
src/fit_em.c
src/rph_phylo_hmm.c
src/eigen.h
src/rph_subst_mods.c
src/bd_phylo_hmm.h
src/phylo_p.c
src/phast_cons.h
src/vector.c
src/rph_phyloP.c
src/tfbs.h
src/version
src/em.c
src/subst_mods.c
src/vector.h
src/local_alignment.c
src/multi_msa.h
src/numerical_opt.c
src/misc.h
src/pssm.h
src/rph_list_of_lists.c
src/memory_handler.c
src/markov_matrix.h
src/indel_history.c
src/indel_history.h
src/lists.c
src/bgc_hmm.h
src/gff.h
src/fit_em.h
src/motif.c
src/phylo_fit.h
src/prob_matrix.h
src/rph_bgc_hmm.c
src/eigen.c
src/phylo_p_print.c
src/markov_matrix.c
src/msa.h
src/rph_tfbs.c
src/tree_likelihoods.c
src/local_alignment.h
src/rph_tree_model.c
src/gap_patterns.h
src/subst_distrib.h
src/fit_feature.c
src/complex_vector.c
src/rph_gff.c
src/complex_matrix.c
src/fit_feature.h
src/category_map.h
src/Makevars.in
src/category_map.c
src/multi_msa.c
src/maf.h
src/wig.c
src/external_libs.h
src/complex_matrix.h
src/rph_util.c
src/gff.c
src/stringsplus.c
src/dgamma.c
src/wig.h
src/numerical_opt.h
src/rph_msa.c
src/bgc_hmm.c
src/tree_model.h
src/memory_handler.h
src/rph_util.h
src/complex.h
src/rph_init.c
src/maf_block.c
src/maf_block.h
src/Makevars.win
src/trees.h
src/hmm.h
src/ms.h
src/stringsplus.h
src/genepred.h
src/motif.h
src/puzzler.h
src/rph_wig.c
src/msa.c
src/genepred.c
src/phylo_fit.c
src/indel_mod.c
src/phylo_hmm.h
src/trees.c
src/phast_cons.c
src/rph_phyloFit.c
src/dgamma.h
src/lists.h
src/tree_likelihoods.h
src/prob_matrix.c
src/prob_vector.c
src/matrix.h
NAMESPACE
R
R/treeModel.R R/phastCons.R R/checkArgs.R R/rphast.R R/phyloP.R R/hmm.R R/plot.R R/feat.R R/optim.R R/phyloFit.R R/msa.R R/bgc.R R/zzz.R R/listOfLists.R R/trees.R
vignettes
vignettes/vignette1.Rnw
vignettes/vignette4.Rnw
vignettes/rphast.bib
vignettes/vignette3.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
configure
ChangeLog
man
man/write.feat.Rd man/branchlength.tree.Rd man/from.pointer.msa.Rd man/apply.bgc.sel.Rd man/as.track.msa.Rd man/add.signals.feat.Rd man/tm.Rd man/ninf.msa.Rd man/phyloP.sph.Rd man/nrow.feat.Rd man/composition.feat.Rd man/extract.feature.msa.Rd man/optim.rphast.Rd man/copy.msa.Rd man/write.wig.Rd man/plot.gene.Rd man/ncol.feat.Rd man/write.msa.Rd man/ncol.msa.Rd man/register.rphast.Rd man/sample.msa.Rd man/get4d.msa.Rd man/translate.msa.Rd man/label.subtree.Rd man/subtree.Rd man/strip.gaps.msa.Rd man/as.pointer.msa.Rd man/copy.feat.Rd man/msa.Rd man/phyloFit.Rd man/classify.muts.bgc.Rd man/coverage.feat.Rd man/nrow.msa.Rd man/col.expected.subs.msa.Rd man/add.ls.mod.Rd man/mod.backgd.tm.Rd man/as.data.frame.feat.Rd man/is.subst.mod.tm.Rd man/postprob.msa.Rd man/as.list.tm.Rd man/pairwise.diff.msa.Rd man/flatten.feat.Rd man/summary.msa.Rd man/phyloP.Rd man/fix.start.stop.feat.Rd man/plot.msa.Rd man/tagval.feat.Rd man/read.msa.Rd man/sub.msa.Rd man/hmm.Rd man/alphabet.msa.Rd man/write.wig.feat.Rd man/rbind.feat.Rd man/summary.feat.Rd man/enrichment.feat.Rd man/write.hmm.Rd man/prune.tree.Rd man/read.wig.Rd man/as.pointer.feat.Rd man/total.expected.subs.msa.Rd man/complement.Rd man/unapply.bgc.sel.Rd man/range.track.Rd man/names.msa.Rd man/set.rate.matrix.tm.Rd man/write.tm.Rd man/print.tm.Rd man/phyloP.prior.Rd man/print.msa.Rd man/range.feat.Rd man/informative.regions.msa.Rd man/summary.tm.Rd man/bgc.informative.Rd man/dim.msa.Rd man/square-bracket-msa.Rd man/print.feat.Rd man/overlap.feat.Rd man/concat.msa.Rd man/likelihood.msa.Rd man/convert.coords.feat.Rd man/subst.mods.Rd man/read.hmm.Rd man/bgc.nucleotide.tests.Rd man/add.UTRs.feat.Rd man/depth.tree.Rd man/read.tm.Rd man/inverse.feat.Rd man/is.msa.Rd man/smooth.wig.Rd man/base.freq.msa.Rd man/is.tm.Rd man/sort.feat.Rd man/gc.content.msa.Rd man/add.introns.feat.Rd man/rename.tree.Rd man/plot.tm.Rd man/get.rate.matrix.params.tm.Rd man/codon.clean.msa.Rd man/read.newick.tree.Rd man/numnodes.tree.Rd man/print.phastBiasResult.Rd man/offset.msa.Rd man/score.hmm.Rd man/dim.feat.Rd man/as.track.wig.Rd man/reverse.complement.msa.Rd man/name.ancestors.Rd man/is.track.Rd man/reflect.phylo.hmm.Rd man/tagval.Rd man/plot.feat.Rd man/summary.tree.Rd man/state.freq.msa.Rd man/numleaf.tree.Rd man/split.feat.Rd man/phastCons.Rd man/phastBias.Rd man/as.track.feat.Rd man/density.feat.Rd man/square-bracket-assign-msa.Rd man/unique.feat.Rd man/read.feat.Rd man/label.branches.Rd man/freq3x4.msa.Rd man/setup.branch.site.tm.Rd man/nothanks.rphast.Rd man/split.by.feature.msa.Rd man/leafnames.tree.Rd man/is.format.msa.Rd man/from.pointer.feat.Rd man/is.ordered.msa.Rd man/fix.semicolon.tree.Rd man/plot.rate.matrix.Rd man/nstate.hmm.Rd man/feat.Rd man/guess.format.msa.Rd man/expected.subs.msa.Rd man/coord.range.msa.Rd man/hist.feat.Rd man/simulate.msa.Rd man/plot.lsmodel.tm.Rd man/rphast-package.Rd man/plot.track.Rd man/bgc.sel.factor.Rd man/rescale.tree.Rd
cleanup
LICENSE
rphast documentation built on May 30, 2017, 5:13 a.m.