DESCRIPTION

Package: megaptera
Type: Package
Title: MEGAPhylogeny Techniques in R
Version: 1.1.6
Date: 2019-02-13
Authors@R: person("Christoph", "Heibl", 
  email = "christoph.heibl@gmx.net",
  role = c("aut", "cre"))
Imports:
    ape,
    bold,
    crul,
    data.table,
    DBI,
    knitr,
    methods,
    parallel,
    RCurl,
    restez,
    rGUIDANCE,
    rmarkdown,
    RPostgreSQL,
    seqinr,
    tools,
    XML
Depends:
    R (>= 3.1),
    ips
Suggests:
    testthat,
    viper
Encoding: UTF-8
Description: Given a set of taxa and markers, the goal is build a complete and
    correct sequence alignment for phylogenetic analysis.
License: GPL (>= 2)
LazyData: true
VignetteBuilder: knitr
Packaged: Wed Feb 13 14:47:54 2019
RoxygenNote: 7.0.2
Collate: 
    'BOLD2megaptera.R'
    'DNAbin2pg.R'
    'EFetchXML.R'
    'MAD.R'
    'NCBI.wrap.R'
    'XML2acc.R'
    'addNbAcc.R'
    'addSingleTip.R'
    'addTips.R'
    'alignGenus.R'
    'alignSisterClades.R'
    'alignSpecies.R'
    'as.Linnean.R'
    'boldLineage.R'
    'boxplotMSA.R'
    'check.TaxAgainstPhy.R'
    'checkBlocks.R'
    'checkExcludedSpec.R'
    'checkIdentityCoverage.R'
    'checkMissingSpec.R'
    'checkSpecLocus.R'
    'checkSpecies.R'
    'checkStatus.R'
    'checkSubset.R'
    'collapseSingles.R'
    'compareToRef.R'
    'comprehensiveGuidetree.R'
    'coverage.R'
    'cropToReference.R'
    'dbChooseRef.R'
    'dbDNA.R'
    'dbDeleteSpec.R'
    'dbExcludeIndet.R'
    'dbExcludeSpec.R'
    'dbIncludeSpec.R'
    'dbMaxGIPerSpec.R'
    'dbPars-class.R'
    'dbPars.R'
    'dbProgress.R'
    'dbReadDNA.R'
    'dbReadLocus.R'
    'dbReadMSA.R'
    'dbReadReference.R'
    'dbReadSequence.R'
    'dbReadTaxomony.R'
    'dbRenameSpecies.R'
    'dbSummaryMSA.R'
    'dbSummaryTaxonomy.R'
    'dbTableNames.R'
    'dbTaxonomy.R'
    'dbUpdateReference.R'
    'dbUpdateReference_Clade.R'
    'dbUpdateSurrogate.R'
    'dbUpdateTaxonomy.R'
    'dbWriteDNA.R'
    'dbWriteMSA.R'
    'dbWriteString.r'
    'dbconnect.R'
    'downloadSequences.R'
    'dropExtendedIngroup.R'
    'extractIGS.R'
    'extractLocus.R'
    'findInFlatfile.R'
    'findRoot.R'
    'formatDF.R'
    'frmt.R'
    'fuzzy.match.R'
    'gbflat2db.R'
    'get3LetterCode.R'
    'getLineage.R'
    'giConsensus.R'
    'harmonizePhyloData.R'
    'higherTaxaOnEdges.R'
    'htmlTable.R'
    'icContingency.R'
    'indet.strings.R'
    'is.Linnean.R'
    'is.alignable.R'
    'is.ingroup.R'
    'locus-class.R'
    'locus.R'
    'locusRef-class.R'
    'locusRef.R'
    'maxDist.R'
    'md5.R'
    'meanCS.R'
    'meanPairwiseIdentity.R'
    'megaptera2Rmarkdown.R'
    'megapteraCSS.R'
    'megapteraInit.R'
    'megapteraPars-class.R'
    'megapteraPars.R'
    'taxon-class.R'
    'taxonGuidetree-class.R'
    'megapteraProj-class.R'
    'megapteraProj.R'
    'myDist.R'
    'ncbiGenome.R'
    'ncbiTaxonomy.R'
    'nonmonophyletic.R'
    'nucleotideOverlap.R'
    'optimizeCoverage.R'
    'optimizeIdentity.R'
    'overlappingPairs2.R'
    'pdfPhyloA0.R'
    'pg2DNAbin.R'
    'proParte.R'
    'prune.phylo.rank.R'
    'rcString.R'
    'refSeqGene.R'
    'robustXMLparse.R'
    'selectMSA.R'
    'setLocus.R'
    'slicePhylo.R'
    'slog.R'
    'specCons.R'
    'speciesConsensus.R'
    'speclist2taxdump.R'
    'splitAlignment.R'
    'splitGiTaxon.R'
    'splitNonoverlapping.R'
    'sql.conform.R'
    'sql.wrap.R'
    'stepA.R'
    'stepB.R'
    'stepBLAST.R'
    'stepBOLD.R'
    'stepBX.R'
    'stepB_eutils.R'
    'stepC.R'
    'stepD.R'
    'stepE.R'
    'stepF.R'
    'stepGBLOCKS.R'
    'stepGUIDANCE.R'
    'stepGenBankFTP.R'
    'stepH.R'
    'stepMAFFT.R'
    'strip.infraspec.R'
    'strip.spec.R'
    'supermatrix.R'
    'supermatrix.mrbayes.R'
    'surrogateTips.R'
    'taxdump2phylo.R'
    'taxdumpAddNode.R'
    'taxdumpChangeParent.R'
    'taxdumpChildren.R'
    'taxdumpDropTip.R'
    'taxdumpHigherRank.R'
    'taxdumpLineage.R'
    'taxdumpMRCA.R'
    'taxdumpManageSynonym.R'
    'taxdumpRankOrder.R'
    'taxdumpSanity.R'
    'taxdumpSubset.R'
    'taxdumpSynonym.R'
    'taxdump_isTerminal.R'
    'taxon.R'
    'taxonGuidetree.R'
    'taxonomy2html.R'
    'term.R'
    'valid.NCBI.taxon.R'
    'whereToInsert.R'
    'wrapSQL.R'