{ "_id": "6a1df5eb1d7bb097a0a5ac76", "Package": "PhyloProfile", "Version": "2.5.1", "Date": "2026-06-01", "Title": "PhyloProfile", "Authors@R": "c(\nperson(\"Vinh\", \"Tran\", role = c(\"aut\", \"cre\"), email = \"tran@bio.uni-frankfurt.de\", comment=c(ORCID=\"0000-0001-6772-7595\")),\nperson(\"Bastian\", \"Greshake Tzovaras\", role = \"aut\", email = \"bgreshake@googlemail.com\"),\nperson(\"Ingo\", \"Ebersberger\", role = \"aut\", email = \"ebersberger@bio.uni-frankfurt.de\"),\nperson(\"Carla\", \"Mölbert\", role = \"ctb\", email = \"carla.moelbert@gmx.de\"))", "Description": "PhyloProfile is a tool for exploring complex phylogenetic\nprofiles. Phylogenetic profiles, presence/absence patterns of\ngenes over a set of species, are commonly used to trace the\nfunctional and evolutionary history of genes across species and\ntime. With PhyloProfile we can enrich regular phylogenetic\nprofiles with further data like sequence/structure similarity,\nto make phylogenetic profiling more meaningful. 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distribution comparison plot", "topics": [ "dataVarDistTaxGroup" ] }, { "page": "dimReduction", "title": "Perform dimension reduction 2D", "topics": [ "dimReduction" ] }, { "page": "distributionTest", "title": "Compare the distribution of 2 numeric vectors", "topics": [ "distributionTest" ] }, { "page": "estimateGeneAge", "title": "Calculate the phylogenetic gene age from the phylogenetic profiles", "topics": [ "estimateGeneAge" ] }, { "page": "fallbackUmap", "title": "Fallback for UMAP in case of insufficient samples", "topics": [ "fallbackUmap" ] }, { "page": "fastaParser", "title": "Parse multi-fasta input file", "topics": [ "fastaParser" ] }, { "page": "featureDistTaxPlot", "title": "Create feature distribution comparison plot", "topics": [ "featureDistTaxPlot" ] }, { "page": "filteredProfile", "title": "An example of a filtered phylogenetic profile", "topics": [ "filteredProfile" ] }, { "page": "filterProfileData", "title": "Filter phylogentic profiles", "topics": [ "filterProfileData" ] }, { "page": "finalProcessedProfile", "title": "An example of a final processed & filtered phylogenetic profile", "topics": [ "finalProcessedProfile" ] }, { "page": "fromInputToProfile", "title": "Complete processing of raw input phylogenetic profiles", "topics": [ "fromInputToProfile" ] }, { "page": "fullProcessedProfile", "title": "An example of a fully processed phylogenetic profile", "topics": [ "fullProcessedProfile" ] }, { "page": "geneAgePlotDf", "title": "Create data for plotting gene ages", "topics": [ "geneAgePlotDf" ] }, { "page": "generateSinglePlot", "title": "Create a single violin distribution plot", "topics": [ "generateSinglePlot" ] }, { "page": "getAllDomainsOma", "title": "Create domain annotation dataframe from a raw OMA dataframe", "topics": [ "getAllDomainsOma" ] }, { "page": "getAllFastaOma", "title": "Get all fasta sequences from a raw OMA dataframe", "topics": [ "getAllFastaOma" ] }, { "page": "getCommonAncestor", "title": "Get all taxa 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best e-value/bitscore", "topics": [ "linearizeArchitecture" ] }, { "page": "mainLongRaw", "title": "An example of a raw long input file", "topics": [ "mainLongRaw" ] }, { "page": "mainTaxonomyRank", "title": "Get all NCBI taxonomy rank names", "topics": [ "mainTaxonomyRank" ] }, { "page": "modifyFeatureName", "title": "Modify feature names", "topics": [ "modifyFeatureName" ] }, { "page": "pairDomainPlotting", "title": "Create architecure plot for a pair of seed and ortholog protein", "topics": [ "pairDomainPlotting" ] }, { "page": "parseDomainInput", "title": "Parse domain input file", "topics": [ "parseDomainInput" ] }, { "page": "parseInfoProfile", "title": "Parsing info for phylogenetic profiles", "topics": [ "parseInfoProfile" ] }, { "page": "performPCA", "title": "Helper function to perform PCA", "topics": [ "performPCA" ] }, { "page": "performUmap", "title": "Helper function to handle UMAP logic", "topics": [ "performUmap" ] }, { "page": "plotDimRed", "title": "Create dimension 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"title": "Sort list of (super)taxa based on a selected reference (super)taxon", "topics": [ "sortInputTaxa" ] }, { "page": "sortTaxaFromTree", "title": "Get sorted supertaxon list based on a rooted taxonomy tree", "topics": [ "sortTaxaFromTree" ] }, { "page": "taxa2dist", "title": "taxa2dist", "topics": [ "taxa2dist" ] }, { "page": "taxonNamesReduced", "title": "NCBI Taxonomy reduced data set", "topics": [ "taxonNamesReduced" ] }, { "page": "taxonomyMatrix", "title": "Taxonomy matrix for experimental data sets", "topics": [ "taxonomyMatrix" ] }, { "page": "taxonomyTableCreator", "title": "Align NCBI taxonomy IDs of list of taxa into a sorted rank list.", "topics": [ "taxonomyTableCreator" ] }, { "page": "varDistTaxPlot", "title": "Create variable distribution comparison plot", "topics": [ "varDistTaxPlot" ] }, { "page": "wideToLong", "title": "Transform input file in wide matrix into long matrix format", "topics": [ "wideToLong" ] }, { "page": "xmlParser", "title": "Parse orthoXML 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