Files in rphast
Interface to 'PHAST' Software for Comparative Genomics

cleanup

MD5

configure.ac

LICENSE

DESCRIPTION

NAMESPACE

configure

ChangeLog

inst/doc/vignette4.pdf inst/doc/vignette3.R inst/doc/vignette3.pdf inst/doc/vignette4.R

inst/doc/vignette1.Rnw

inst/doc/vignette1.R

inst/doc/vignette4.Rnw

inst/doc/vignette3.Rnw

inst/extdata/examples.zip

inst/extdata/NRSF.zip

vignettes/rphast.bib

vignettes/vignette1.Rnw

vignettes/vignette4.Rnw

vignettes/vignette3.Rnw

R/optim.R R/phyloP.R R/zzz.R R/hmm.R R/trees.R R/phastCons.R R/plot.R R/msa.R R/feat.R R/rphast.R R/checkArgs.R R/bgc.R R/phyloFit.R R/treeModel.R R/listOfLists.R

src/phylo_p_print.c

src/puzzler.h

src/fit_feature.c

src/matrix.c

src/rph_util.c

src/complex_vector.c

src/vector.c

src/phylo_hmm.c

src/hmm.h

src/hmm.c

src/ms.h

src/indel_history.c

src/bgc_hmm.h

src/rph_list_of_lists.c

src/gff.h

src/local_alignment.c

src/rph_phyloP.c

src/list_of_lists.c

src/gap_patterns.c

src/maf_block.h

src/tree_likelihoods.c

src/em.c

src/indel_mod.h

src/matrix.h

src/subst_mods.h

src/rph_wig.c

src/external_libs.h

src/tree_model.h

src/phylo_p_print.h

src/complex_matrix.c

src/fit_column.h

src/tfbs.c

src/rph_tfbs.c

src/queues.h

src/list_of_lists.h

src/Makevars.win

src/category_map.h

src/wig.c

src/genepred.h

src/em.h

src/memory_handler.c

src/phylo_hmm.h

src/phylo_fit.c

src/lists.c

src/rph_msa.c

src/tree_model.c

src/maf.h

src/phast_cons.c

src/sufficient_stats.c

src/numerical_opt.h

src/misc.h

src/vector.h

src/tfbs.h

src/prob_matrix.c

src/phylo_fit.h

src/multi_msa.h

src/rph_gff.c

src/pbs_code.h

src/pssm.h

src/fit_feature.h

src/markov_matrix.c

src/subst_distrib.c

src/rph_phylo_hmm.c

src/multi_msa.c

src/bgc_hmm.c

src/rph_bgc_hmm.c

src/markov_matrix.h

src/fit_column.c

src/hashtable.c

src/hashtable.h

src/prob_vector.c

src/msa.h

src/trees.h

src/motif.h

src/eigen.c

src/maf.c

src/dgamma.h

src/bd_phylo_hmm.h

src/rph_util.h

src/rph_phyloFit.c

src/complex.h

src/indel_history.h

src/trees.c

src/phast_cons.h

src/dgamma.c

src/eigen.h

src/rph_hmm.c

src/memory_handler.h

src/rph_tree_model.c

src/phylo_p.c

src/subst_mods.c

src/complex_vector.h

src/local_alignment.h

src/category_map.c

src/rph_init.c

src/msa.c

src/rph_trees.c

src/motif.c

src/sufficient_stats.h

src/bed.c

src/Makevars.in

src/version

src/stringsplus.c

src/subst_distrib.h

src/gap_patterns.h

src/genepred.c

src/prob_matrix.h

src/misc.c

src/numerical_opt.c

src/prob_vector.h

src/simplex_grid.h

src/tree_likelihoods.h

src/bed.h

src/phylo_p.h

src/fit_em.h

src/stringsplus.h

src/stacks.h

src/gff.c

src/wig.h

src/complex_matrix.h

src/rph_category_map.c

src/rph_subst_mods.c

src/maf_block.c

src/indel_mod.c

src/fit_em.c

src/rph_phastCons.c

src/lists.h

man/alphabet.msa.Rd man/branchlength.tree.Rd man/setup.branch.site.tm.Rd man/from.pointer.msa.Rd man/inverse.feat.Rd man/coverage.feat.Rd man/as.track.feat.Rd man/phastBias.Rd man/rename.tree.Rd man/phyloP.Rd man/likelihood.msa.Rd man/tagval.Rd man/get4d.msa.Rd man/add.introns.feat.Rd man/as.data.frame.feat.Rd man/summary.tree.Rd man/offset.msa.Rd man/name.ancestors.Rd man/label.branches.Rd man/freq3x4.msa.Rd man/sample.msa.Rd man/add.signals.feat.Rd man/rphast-package.Rd man/summary.feat.Rd man/coord.range.msa.Rd man/leafnames.tree.Rd man/write.wig.feat.Rd man/ncol.msa.Rd man/write.wig.Rd man/is.tm.Rd man/read.tm.Rd man/total.expected.subs.msa.Rd man/rbind.feat.Rd man/prune.tree.Rd man/fix.start.stop.feat.Rd man/ninf.msa.Rd man/density.feat.Rd man/extract.feature.msa.Rd man/concat.msa.Rd man/read.msa.Rd man/nstate.hmm.Rd man/nrow.feat.Rd man/translate.msa.Rd man/write.hmm.Rd man/simulate.msa.Rd man/dim.msa.Rd man/smooth.wig.Rd man/nrow.msa.Rd man/tm.Rd man/rescale.tree.Rd man/depth.tree.Rd man/plot.msa.Rd man/phyloFit.Rd man/read.newick.tree.Rd man/bgc.sel.factor.Rd man/plot.track.Rd man/plot.gene.Rd man/hist.feat.Rd man/as.pointer.feat.Rd man/unapply.bgc.sel.Rd man/plot.lsmodel.tm.Rd man/feat.Rd man/print.msa.Rd man/optim.rphast.Rd man/read.hmm.Rd man/phastCons.Rd man/reflect.phylo.hmm.Rd man/plot.tm.Rd man/convert.coords.feat.Rd man/phyloP.prior.Rd man/pairwise.diff.msa.Rd man/write.msa.Rd man/split.by.feature.msa.Rd man/mod.backgd.tm.Rd man/composition.feat.Rd man/apply.bgc.sel.Rd man/unique.feat.Rd man/subtree.Rd man/col.expected.subs.msa.Rd man/reverse.complement.msa.Rd man/complement.Rd man/label.subtree.Rd man/print.tm.Rd man/numnodes.tree.Rd man/is.subst.mod.tm.Rd man/square-bracket-msa.Rd man/bgc.nucleotide.tests.Rd man/write.feat.Rd man/tagval.feat.Rd man/as.pointer.msa.Rd man/names.msa.Rd man/range.track.Rd man/summary.msa.Rd man/square-bracket-assign-msa.Rd man/read.wig.Rd man/state.freq.msa.Rd man/codon.clean.msa.Rd man/score.hmm.Rd man/sub.msa.Rd man/guess.format.msa.Rd man/gc.content.msa.Rd man/classify.muts.bgc.Rd man/add.UTRs.feat.Rd man/print.feat.Rd man/is.track.Rd man/msa.Rd man/as.track.wig.Rd man/hmm.Rd man/is.msa.Rd man/base.freq.msa.Rd man/as.track.msa.Rd man/informative.regions.msa.Rd man/from.pointer.feat.Rd man/bgc.informative.Rd man/copy.msa.Rd man/write.tm.Rd man/range.feat.Rd man/get.rate.matrix.params.tm.Rd man/read.feat.Rd man/subst.mods.Rd man/dim.feat.Rd man/summary.tm.Rd man/is.ordered.msa.Rd man/add.ls.mod.Rd man/sort.feat.Rd man/enrichment.feat.Rd man/flatten.feat.Rd man/overlap.feat.Rd man/copy.feat.Rd man/phyloP.sph.Rd man/set.rate.matrix.tm.Rd man/ncol.feat.Rd man/split.feat.Rd man/numleaf.tree.Rd man/is.format.msa.Rd man/plot.feat.Rd man/strip.gaps.msa.Rd man/plot.rate.matrix.Rd man/expected.subs.msa.Rd man/print.phastBiasResult.Rd man/fix.semicolon.tree.Rd man/postprob.msa.Rd man/register.rphast.Rd man/nothanks.rphast.Rd man/as.list.tm.Rd

build/vignette.rds

tests/optim.examples.R tests/phyloP.examples.R tests/msa.examples.R tests/feat.examples.R

rphast documentation built on May 1, 2019, 9:26 p.m.

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rphast
Interface to 'PHAST' Software for Comparative Genomics

Files in rphast
Interface to 'PHAST' Software for Comparative Genomics

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rphast Interface to 'PHAST' Software for Comparative Genomics

Files in rphast Interface to 'PHAST' Software for Comparative Genomics

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rphast
Interface to 'PHAST' Software for Comparative Genomics

Files in rphast
Interface to 'PHAST' Software for Comparative Genomics