Files in heibl/megaptera

MEGAPhylogeny Techniques in R

.Rbuildignore

.gitignore

DESCRIPTION

NAMESPACE

R/0-scripts/0-scripts.Rproj

R/BOLD2megaptera.R R/DNAbin2pg.R 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/as.Linnean.R R/boldLineage.R R/boxplotMSA.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/checkSubset.R R/collapseSingles.R R/compareToRef.R R/comprehensiveGuidetree.R R/coverage.R R/cropToReference.R R/dbChooseRef.R R/dbDNA.R R/dbDeleteSpec.R R/dbExcludeIndet.R R/dbExcludeSpec.R R/dbIncludeSpec.R R/dbMaxGIPerSpec.R R/dbPars-class.R R/dbPars.R R/dbProgress.R R/dbReadDNA.R R/dbReadLocus.R R/dbReadMSA.R R/dbReadReference.R R/dbReadSequence.R R/dbReadTaxomony.R R/dbRenameSpecies.R R/dbSummaryMSA.R R/dbSummaryTaxonomy.R R/dbTableNames.R R/dbTaxonomy.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/downloadSequences.R R/dropExtendedIngroup.R

R/exclude_me

R/extractIGS.R R/extractLocus.R R/findInFlatfile.R R/findRoot.R R/formatDF.R R/frmt.R R/fuzzy.match.R R/gbflat2db.R R/get3LetterCode.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/meanCS.R R/meanPairwiseIdentity.R R/megaptera2Rmarkdown.R R/megapteraCSS.R R/megapteraInit.R R/megapteraPars-class.R R/megapteraPars.R R/megapteraProj-class.R R/megapteraProj.R R/myDist.R R/ncbiGenome.R R/ncbiTaxonomy.R R/nonmonophyletic.R R/nucleotideOverlap.R R/optimizeCoverage.R R/optimizeIdentity.R R/overlappingPairs2.R R/pdfPhyloA0.R R/pg2DNAbin.R R/proParte.R R/prune.phylo.rank.R R/rcString.R R/refSeqGene.R R/robustXMLparse.R R/selectMSA.R R/setLocus.R R/slicePhylo.R R/slog.R R/specCons.R R/speciesConsensus.R R/speclist2taxdump.R R/splitAlignment.R R/splitGiTaxon.R R/splitNonoverlapping.R R/sql.conform.R R/sql.wrap.R R/stepA.R R/stepB.R R/stepBLAST.R R/stepBOLD.R R/stepBX.R R/stepB_eutils.R R/stepC.R R/stepD.R R/stepE.R R/stepF.R R/stepGBLOCKS.R R/stepGUIDANCE.R R/stepGenBankFTP.R R/stepH.R R/stepMAFFT.R R/strip.infraspec.R R/strip.spec.R R/supermatrix.R R/supermatrix.mrbayes.R R/surrogateTips.R

R/taxdump2phylo

R/taxdump2phylo.R R/taxdumpAddNode.R R/taxdumpChangeParent.R R/taxdumpChildren.R R/taxdumpDropTip.R R/taxdumpHigherRank.R R/taxdumpLineage.R R/taxdumpMRCA.R R/taxdumpManageSynonym.R R/taxdumpRankOrder.R R/taxdumpSanity.R R/taxdumpSubset.R R/taxdumpSynonym.R R/taxdump_isTerminal.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

data/cetacea.rda

data/data.Rproj

data/input.rda

deprecated/Getting-started.rnw

deprecated/Getting-started.tex

deprecated/NCBIeaa.Rd

deprecated/NCBIeaa.rda

deprecated/addRanks.R deprecated/alignSubtree.R deprecated/comprehensiveGuidetree_OLD.R deprecated/dbPReadDNA.R deprecated/dbPars-class.Rd deprecated/dbReadTaxomony_OLD.R deprecated/dbUpdateTaxonomy_OLD.R deprecated/decomposePhylo.R deprecated/findRoot.R deprecated/mergeSubMSA.R deprecated/mergeSubMSA2.R deprecated/revCompTest.R deprecated/sortRanks.R deprecated/stepA.R deprecated/stepF.R deprecated/stepGG.R deprecated/stepPASTAin.R deprecated/stepPASTAout.R deprecated/taxdump2phylo.R deprecated/taxdumpDaughters.R dev/DEV-checkSubset.R dev/DEV-guidance2-into-megaptera.R dev/DEV-new-MSA-tab.R dev/debug-comprehensiveGuidetree.R dev/ns-raus.R dev/taxon-nodelabels.R

inst/CITATION

inst/NEWS.Rd

man/BOLD2megaptera.Rd man/addSingleTip.Rd man/addTips.Rd man/cetacea.Rd man/checkBlocks.Rd man/checkIdentityCoverage.Rd man/checkMissingSpec.Rd man/checkSpecLocus.Rd man/checkSpecies.Rd man/checkSubset.Rd man/collapseSingles.Rd man/comprehensiveGuidetree.Rd man/dbDNA.Rd man/dbManipulateSpec.Rd man/dbMaxGIPerSpec.Rd man/dbPars-class.Rd man/dbPars.Rd man/dbReadLocus.Rd man/dbReadMSA.Rd man/dbRenameSpecies.Rd man/dbSummaryTaxonomy.Rd man/dbTaxonomy.Rd man/dropExtendedIngroup.Rd man/findInFlatfile.Rd man/findRoot.Rd man/gbflat2db.Rd man/get3LetterCode.Rd man/higherTaxaOnEdges.Rd man/icContingency.Rd man/indet.strings.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/megapteraInit.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/pdfPhyloA0.Rd man/pg2DNAbin.Rd man/prune.phylo.rank.Rd man/selectMSA.Rd man/setLocus.Rd man/slicePhylo.Rd man/speclist2taxdump.Rd man/stepA.Rd man/stepB.Rd man/stepBLAST.Rd man/stepBX.Rd man/stepC.Rd man/stepD.Rd man/stepE.Rd man/stepF.Rd man/stepGBLOCKS.Rd man/stepGUIDANCE.Rd man/stepGenBankFTP.Rd man/stepH.Rd man/stepMAFFT.Rd man/strip.infraspec.Rd man/strip.spec.Rd man/supermatrix.Rd man/surrogateTips.Rd man/taxdump2phylo.Rd man/taxdumpAddNode.Rd man/taxdumpChangeParent.Rd man/taxdumpChildren.Rd man/taxdumpDropTip.Rd man/taxdumpHigherRank.Rd man/taxdumpLineage.Rd man/taxdumpMRCA.Rd man/taxdumpManageSynonym.Rd man/taxdumpRankOrder.Rd man/taxdumpSanity.Rd man/taxdumpSubset.Rd man/taxdumpSynonym.Rd man/taxdump_isTerminal.Rd man/taxon-class.Rd man/taxon.Rd man/taxonGuidetree-class.Rd

megaptera.Rproj

tests/testthat/test_string_operations.R

vignettes/.gitignore

vignettes/Cetacea.Rmd

vignettes/biology.bib

vignettes/journal-of-biogeography.csl

heibl/megaptera documentation built on Jan. 17, 2021, 3:34 a.m.