EvoWeaver Supplemental Datafiles

This dataset contains additional files related to EvoWeaver. The following are included: ProteinComplexTrees.RData: All phylogenetic trees for Complexes benchmark. These are stored in a list object with one tree per gene group. ModulesEvoWeaver.RData: EvoWeaver object for Modules benchmark, containing phylogenetic trees for the Modules and Multiclass benchmark. `ModulePredAllPairs.RData` was made using this object. CORUM_Blast_Results.RData: All results from pairwise BLAST of proteomes against human reference genes. CORUM_proteomes.zip: all proteomes for all organisms used. Some of these are length 0, if an assembly could not be programatically found or retrieval failed to work. CORUMOrthogroupsWithIndices.RData: Orthogroups for the CORUM benchmark with gene index data included KOsWithPositions.RData: Gene index data for KO groups used in this study ModsWithPositions.RData: Gene index data for modules used in this study AllKEGGModules.RData: KEGG module taxonomy, names, and pathways for all modules used at time of download KEGGModuleComplexes.RData: All complexes in a KEGG module at time of download KEGGModuleDefinitions.RData: All KEGG module definitions at time of download ModulesPositionData.RData: Gene index information for Modules benchmark COG.links.detailed.v12.0.txt.tar.gz: STRING evidence streams between COGs (compressed, 1.44GB uncompressed) COG.mappings.v12.0.txt.tar.gz: STRING COG definitions (compressed, 5.80GB uncompressed) AllHumanGenes.fa: Human gene sequences used for BLASTing against in the CORUM benchmark AllKEGGCDSs.RData: all sets of available genes from all genomes used in KEGG. Note that internal algorithm names may not exactly match those in published material due to computational requirements (e.g., difficulty naming functions/variables with special characters). See the GitHub page for a description of which internal names correspond to algorithms in the text.