addDimRedTaxaColors	addDimRedTaxaColors
addFeatureColors	addFeatureColors
addRankDivisionPlot	addRankDivisionPlot
calcPresSpec	calcPresSpec
checkColorPalette	checkColorPalette
checkInputValidity	checkInputValidity
checkNewick	checkNewick
checkOmaID	checkOmaID
checkOverlapDomains	checkOverlapDomains
clusterDataDend	clusterDataDend
compareMedianTaxonGroups	compareMedianTaxonGroups
compareTaxonGroups	compareTaxonGroups
createArchiPlot	createArchiPlot
createDimRedPlotData	createDimRedPlotData
createGeneAgePlot	createGeneAgePlot
createLongMatrix	createLongMatrix
createPercentageDistributionData	createPercentageDistributionData
createProfileFromOma	createProfileFromOma
createUnrootedTree	createUnrootedTree
createVarDistPlot	createVarDistPlot
createVariableDistributionData	createVariableDistributionData
createVariableDistributionDataSubset	createVariableDistributionDataSubset
dataCustomizedPlot	dataCustomizedPlot
dataFeatureTaxGroup	dataFeatureTaxGroup
dataMainPlot	dataMainPlot
dataVarDistTaxGroup	dataVarDistTaxGroup
dimReduction	dimReduction
distributionTest	distributionTest
estimateGeneAge	estimateGeneAge
fallbackUmap	fallbackUmap
fastaParser	fastaParser
featureDistTaxPlot	featureDistTaxPlot
filteredProfile	filteredProfile
filterProfileData	filterProfileData
finalProcessedProfile	finalProcessedProfile
fromInputToProfile	fromInputToProfile
fullProcessedProfile	fullProcessedProfile
geneAgePlotDf	geneAgePlotDf
generateSinglePlot	generateSinglePlot
getAllDomainsOma	getAllDomainsOma
getAllFastaOma	getAllFastaOma
getCommonAncestor	getCommonAncestor
getCoreGene	getCoreGene
getDataClustering	getDataClustering
getDataForOneOma	getDataForOneOma
getDendrogram	getDendrogram
getDistanceMatrix	getDistanceMatrix
getDomainFolder	getDomainFolder
getFastaFromFasInput	getFastaFromFasInput
getFastaFromFile	getFastaFromFile
getFastaFromFolder	getFastaFromFolder
getIDsRank	getIDsRank
getInputTaxaID	getInputTaxaID
getInputTaxaName	getInputTaxaName
getNameList	getNameList
getOmaDataForOneOrtholog	getOmaDataForOneOrtholog
getOmaDomainFromURL	getOmaDomainFromURL
getOmaMembers	getOmaMembers
getQualColForVector	getQualColForVector
getSelectedFastaOma	getSelectedFastaOma
getSelectedTaxonNames	getSelectedTaxonNames
getTaxHierarchy	getTaxHierarchy
getTaxonomyInfo	getTaxonomyInfo
getTaxonomyMatrix	getTaxonomyMatrix
getTaxonomyRanks	getTaxonomyRanks
gridArrangeSharedLegend	gridArrangeSharedLegend
groupLabelDimRedData	groupLabelDimRedData
heatmapPlotting	heatmapPlotting
heatmapPlottingFast	heatmapPlottingFast
highlightProfilePlot	highlightProfilePlot
id2name	id2name
idList	idList
joinPlotMergeLegends	joinPlotMergeLegends
linearizeArchitecture	linearizeArchitecture
mainLongRaw	mainLongRaw
mainTaxonomyRank	mainTaxonomyRank
modifyFeatureName	modifyFeatureName
pairDomainPlotting	pairDomainPlotting
parseDomainInput	parseDomainInput
parseInfoProfile	parseInfoProfile
performUmap	performUmap
plotDimRed	plotDimRed
plotDimRed3D	plotDimRed3D
ppTaxonomyMatrix	ppTaxonomyMatrix
ppTree	ppTree
prepareDimRedData	prepareDimRedData
processNcbiTaxonomy	processNcbiTaxonomy
processOrthoID	processOrthoID
profileWithTaxonomy	profileWithTaxonomy
qualitativeColours	qualitativeColours
rankIndexing	rankIndexing
rankList	rankList
reduceProfile	reduceProfile
resolveOverlapFeatures	resolveOverlapFeatures
runPhyloProfile	runPhyloProfile
singleDomainPlotting	singleDomainPlotting
sortDomains	sortDomains
sortDomainsByList	sortDomainsByList
sortInputTaxa	sortInputTaxa
sortTaxaFromTree	sortTaxaFromTree
taxa2dist	taxa2dist
taxonNamesReduced	taxonNamesReduced
taxonomyMatrix	taxonomyMatrix
taxonomyTableCreator	taxonomyTableCreator
varDistTaxPlot	varDistTaxPlot
wideToLong	wideToLong
xmlParser	xmlParser
