Files in heibl/megaptera
MEGAPhylogeny Techniques in R

.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/EFetchXML.R R/MAD.R R/NCBI.wrap.R R/XML2acc.R R/addNbAcc.R R/addSingleTip.R R/addTips.R R/alignGenus.R R/alignSisterClades.R R/alignSpecies.R R/alignSubtree.R R/as.Linnean.R R/boxplotMSA.R R/changeSpecName.R R/check.TaxAgainstPhy.R R/checkBlocks.R R/checkExcludedSpec.R R/checkIdentityCoverage.R R/checkMissingSpec.R R/checkSpecLocus.R R/checkSpecies.R R/checkStatus.R R/compareToRef.R R/comprehensiveGuidetree.R R/coverage.R R/cropToReference.R R/dbAutofillTaxonomy.R R/dbChooseRef.R R/dbDeleteSpec.R R/dbExcludeIndet.R R/dbExcludeSpec.R R/dbIncludeSpec.R R/dbMaxGIPerSpec.R R/dbPReadDNA.R R/dbPars-class.R R/dbPars.R R/dbProgress.R R/dbReadDNA.R R/dbReadLocus.R R/dbReadReference.R R/dbReadTaxomony.R R/dbSummaryMSA.R R/dbSummaryTaxonomy.R R/dbTableNames.R R/dbUpdateReference.R R/dbUpdateReference_Clade.R R/dbUpdateSurrogate.R R/dbUpdateTaxonomy.R R/dbWriteDNA.R R/dbWriteMSA.R R/dbWriteString.r R/dbconnect.R R/decomposePhylo.R R/downloadSequences.R R/dropExtendedIngroup.R R/extractIGS.R R/extractLocus.R R/findRoot.R R/fixTaxonomy.R R/ftp2postgres.R R/fuzzy.match.R R/getLineage.R R/giConsensus.R R/harmonizePhyloData.R R/higherTaxaOnEdges.R R/htmlTable.R R/icContingency.R R/indet.strings.R R/is.Linnean.R R/is.alignable.R R/is.ingroup.R R/locus-class.R R/locus.R R/locusRef-class.R R/locusRef.R R/maxDist.R R/md5.R R/meanPairwiseIdentity.R R/megaptera2Rmarkdown.R R/megapteraPars-class.R R/megapteraPars.R R/megapteraProj-class.R R/megapteraProj.R R/mergeSubMSA.R R/mergeSubMSA2.R R/myDist.R R/ncbiGenome.R R/ncbiTaxonomy.R R/nonmonophyletic.R R/nucleotideOverlap.R R/opal.merge.R R/optimizeCoverage.R R/optimizeIdentity.R R/overlappingPairs2.R R/pdfPhyloA0.R R/plotPhyloWithClassification.R R/proParte.R R/prune.phylo.rank.R R/robustXMLparse.R R/setLocus.R R/slicePhylo.R R/slog.R R/specCons.R R/speciesConsensus.R R/splitAlignment.R R/splitGiTaxon.R R/splitNonoverlapping.R R/sql.conform.R R/sql.wrap.R R/sqlTaxonomyHeader.R R/stepA.R R/stepB.R R/stepBOLD.R R/stepBX.R R/stepC.R R/stepD.R R/stepE.R R/stepF.R R/stepG.R R/stepGG.R R/stepH.R R/stepI.R R/stepPASTA.R R/stepPASTAin.R R/stepPASTAout.R R/stepPOLENTA.R R/strip.infraspec.R R/strip.spec.R R/supermatrix.R R/supermatrix.mrbayes.R R/surrogateTips.R R/tax2tree.R R/taxdump2phylo.R R/taxdumpAddNode.R R/taxdumpDaughters.R R/taxdumpDropTip.R R/taxdumpHigherRank.R R/taxdumpLineage.R R/taxdumpMRCA.R R/taxdumpSubset.R R/taxon-class.R R/taxon.R R/taxonGuidetree-class.R R/taxonGuidetree.R R/taxonomy2html.R R/term.R R/valid.NCBI.taxon.R R/whereToInsert.R R/wrapSQL.R README.md
TODO
build/vignette.rds
data/NCBIeaa.rda
data/araneae.megapteraProj
data/cetacea.rda
data/input.rda
deprecated/Getting-started.rnw
deprecated/Getting-started.tex
deprecated/addRanks.R deprecated/comprehensiveGuidetree_OLD.R deprecated/dbReadTaxomony_OLD.R deprecated/dbUpdateTaxonomy_OLD.R deprecated/findRoot.R deprecated/revCompTest.R deprecated/sortRanks.R deprecated/stepA.R deprecated/taxdump2phylo.R deprecated/taxdumpDaughters.R
inst/CITATION
inst/NEWS.Rd
inst/doc/Cetacea.R inst/doc/Cetacea.Rmd
inst/doc/Cetacea.html
inst/megaptera-synopsis.aux
inst/megaptera-synopsis.log
inst/megaptera-synopsis.out
inst/megaptera-synopsis.pdf
inst/megaptera-synopsis.synctex.gz
inst/megaptera-synopsis.tex
inst/megaptera-synopsis.toc
man/.Rapp.history
man/NCBIeaa.Rd man/addSingleTip.Rd man/addTips.Rd man/cetacea.Rd man/checkIdentityCoverage.Rd man/checkMissingSpec.Rd man/checkSpecLocus.Rd man/checkSpecies.Rd man/comprehensiveGuidetree.Rd man/dbDNA.Rd man/dbManipulateSpec.Rd man/dbPars-class.Rd man/dbPars.Rd man/dbReadLocus.Rd man/dbTaxonomy.Rd man/dropExtendedIngroup.Rd man/findRoot.Rd man/higherTaxaOnEdges.Rd man/icContingency.Rd man/is.ingroup.Rd man/locus-class.Rd man/locus.Rd man/locusRef-class.Rd man/megaptera-internal.Rd man/megaptera-package.Rd man/megaptera2Rmarkdown.Rd man/megapteraPars-class.Rd man/megapteraPars.Rd man/megapteraProj-class.Rd man/megapteraProj.Rd man/ncbiGenome.Rd man/ncbiTaxonomy.Rd man/optimize.Rd man/plotPhyloWithClassification.Rd man/prune.phylo.rank.Rd man/setLocus.Rd man/stepA.Rd man/stepB.Rd man/stepBX.Rd man/stepC.Rd man/stepD.Rd man/stepE.Rd man/stepF.Rd man/stepG.Rd man/stepH.Rd man/stepI.Rd man/strip.infraspec.Rd man/strip.spec.Rd man/supermatrix.Rd man/surrogateTips.Rd man/taxdump2phylo.Rd man/taxdumpAddNode.Rd man/taxdumpDaughters.Rd man/taxdumpLineage.Rd man/taxdumpMRCA.Rd man/taxdumpSubset.Rd man/taxon-class.Rd man/taxon.Rd man/taxonGuidetree-class.Rd
megaptera.Rproj
tests/testthat/testthat.R vignettes/Cetacea.Rmd
vignettes/biology.bib
vignettes/journal-of-biogeography.csl
heibl/megaptera documentation built on Oct. 13, 2017, 8:47 p.m.