`?T|      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~None24&Datastructure for Gene2Accession tableSimple Gene2Accession table >Datastructure for entries of Taxonomy database dump nodes file$8Taxonomic ranks: NCBI uses the uncommon Speciessubgroup O>Datastructure for entries of Taxonomy database dump names fileUDDatastructure for entries of Taxonomy database dump mergednodes fileY@Datastructure for entries of Taxonomy database dump gencode file`ADatastructure for entries of Taxonomy database dump division filefFDatastructure for entries of Taxonomy database dump deleted nodes fileiBDatastructure for entries of Taxonomy database dump citations filerGNCBI Taxonomy database dump hierachichal data structure as defined in 6ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump_readme.txt{SLineage Taxons denote all parent Taxonomy nodes of a node retrieved by Entrez fetch/Data structure for Entrez taxonomy fetch result"Datastructure for tree comparisonsSimpleTaxon only contains the most relevant fields of a taxonomy entry. For all annotaded fields use the Taxon datatype and its associated functions  !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~  !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~{|}~rstuvwxyzijklmnopqfgh`abcdeYZ[\]^_UVWXOPQRST$NMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&% !"#   !"#$*NMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%OPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ None$NCBI taxonomy dump nodes and names in the input directory path are parsed and a SimpleTaxon tree with scientific names for each node is generated. oNCBI taxonomy dump nodes and names in the input directory path are parsed and a SimpleTaxon tree is generated. nNCBI taxonomy dump nodes and names in the input directory path are parsed and a SimpleTaxon tree is generated.(parse NCBITaxCitations from input string@parse NCBITaxCitations from input filePath 'parse NCBITaxDelNodes from input string?parse NCBITaxDelNodes from input filePath 'parse NCBITaxDivisons from input string?parse NCBITaxDivisons from input filePath 'parse NCBITaxGenCodes from input string?parse NCBITaxGenCodes from input filePath *parse NCBITaxMergedNodes from input stringBparse NCBITaxMergedNodes from input filePath $parse NCBITaxNames from input string<parse NCBITaxNames from input filePath $parse NCBITaxNames from input string@parse NCBITaxCitations from input filePath *parse NCBISimpleTaxNames from input string@parse NCBITaxCitations from input filePath #Parse the input as NCBITax datatypeExtract a subtree correpsonding to input node paths to root. Only nodes in level number distance to root are included. Used in Ids2TreeCompare tool.Extract a subtree corresponding to input node paths to root. Only nodes in level number distance to root are included. Used in Ids2Tree tool.Extract a subtree corresponding to input node paths to root. If a Rank is provided, all node that are less or equal are omitted'Extract parent node with specified Rank-Filter nodes by distance from root >Find only taxons of a specific rank in a list of input taxons 9Filter a list of input taxons for a minimal provided rank>Returns path between 2 maybe nodes. Used in TreeDistance tool.0Draw graph in dot format. Used in Ids2Tree tool.GDraw tree comparison graph in dot format. Used in Ids2TreeCompare tool.fColors from color list are selected according to in which of the compared trees the node is contained.SA color list is sampled from the spectrum according to how many trees are compared.EWrite tree representation either as dot or json to provided file pathWrite tree representation as dot to provided file path. Graphviz tools like dot can be applied to the written .dot file to generate e.g. svg-format images.mWrite tree representation as json to provided file path. You can visualize the result for example with 3Djs.Dcheck a list of parsing results for presence of Left aka Parse errorF  !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~F      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOOPQRSTTUVWWXYZ[\]]^_`abbcddefghijkllmnopqrsttuvwxxyz{{|}~Taxonomy-1.0.1Bio.TaxonomyData Bio.TaxonomyGene2Accession taxIdEntrygeneIDstatusrnaNucleotideAccessionVersionrnaNucleotideGiproteinAccessionVersion proteinGi!genomicNucleotideAccessionVersiongenomicNucleotideGi"startPositionOnTheGenomicAccession endPositionOnTheGenomicAccession orientationassemblymaturePeptideAccessionVersionmaturePeptideGiSimpleGene2AccessionsimpleTaxIdEntry'simpleGenomicNucleotideAccessionVersionTaxNodetaxId parentTaxIdrankemblCodenodeDivisionIdinheritedDivFlagnodeGeneticCodeIdinheritedGCFlagmitochondrialGeneticCodeIdinheritedMGCFlaggenBankHiddenFlaghiddenSubtreeRootFlag nodeCommentsRankDomain SuperkingdomKingdom Subkingdom Infrakingdom SuperphylumPhylum Subphylum Infraphylum Microphylum SuperclassClassSubclass Infraclass ParvclassLegionCohort Magnorder SuperorderOrderSuborder Infraorder Parvorder SuperfamilyFamily Subfamily SupertribeTribeSubtribeGenusSubgenusSectionSeries Superspecies SpeciesgroupSpeciesSpeciessubgroup Subspecies InfraspeciesVarietyFormNorankTaxName nameTaxIdnameTxt uniqueName nameClass TaxMergedNodeoldTaxIdnewTaxId TaxGenCode geneticCodeId abbreviation geneCodeNamecdestarts TaxDivision divisionId divisionCDE divisonNamedivisionComments TaxDelNodedelTaxId TaxCitationcitIdcitKeypubmedId medlineIdurltext taxIdList NCBITaxDump taxCitations taxDelNodes taxDivisions taxGenCodestaxMergedNodestaxNamestaxNodes LineageTaxon lineageTaxIdlineageScienticName lineageRank TaxonNameclassCDEdispNameTaxon taxonTaxIdtaxonScientificNametaxonParentTaxId taxonRankdivision geneticCodemitoGeneticCodelineage lineageEx createDate updateDatepubDate CompareTaxoncompareScientificName compareRankinTree SimpleTaxon simpleTaxIdsimpleScientificNamesimpleParentTaxId simpleRank readsRanksimpleTaxonJSONValue $fToJSONGr $fReadRankreadNamedTaxonomy readTaxonomy parseTaxonomyparseNCBITaxCitationsreadNCBITaxCitationsparseNCBITaxDelNodesreadNCBITaxDelNodesparseNCBITaxDivisionsreadNCBITaxDivisionsparseNCBITaxGenCodesreadNCBITaxGenCodesparseNCBITaxMergedNodesreadNCBITaxMergedNodesparseNCBITaxNamesreadNCBITaxNamesparseNCBITaxNodesreadNCBITaxNodesparseNCBISimpleTaxonsreadNCBISimpleTaxonsreadNCBITaxonomyDatabasecompareSubTreesextractTaxonomySubTreebyLevelextractTaxonomySubTreebyRankgetParentbyRank safeNodePath drawTaxonomydrawTreeComparison writeTree writeDotTree writeJsonTreefilterNodesByLevelfindNodeByRankfilterNodesByRank selectColors makeColorList checkParsinggenParserTaxonomyGraphgenParserNamedTaxonomyGraphsetNodeScientificNamegenParserGraphNodeEdgegenParserNCBITaxCitationsgenParserNCBITaxDelNodesgenParserNCBITaxDivisonsgenParserNCBITaxGenCodesgenParserNCBITaxMergedNodesgenParserNCBITaxNamesgenParserNCBITaxNodesgenParserNCBISimpleTaxonsgenParserNCBITaxCitationgenParserNCBITaxDelNodegenParserNCBITaxDivisiongenParserNCBITaxGenCodegenParserNCBITaxMergedNodegenParserNCBITaxNamegenParserNCBISimpleTaxongenParserNCBITaxNodeannotateTaxonsDifferenceannotateTaxonDifferencegetPath sortByNodeIDreadIntreadBoolreadRankgenParserTaxIdListgenParserTaxURLconcatenateURLPartsmaybeStringConcatreadEncodedFileparseFromFileEncISO88591extractParseError