The data files were generated from the PhyloGenes 4.0 release (see release notes here). About the two zip files: 1. phyloXML.zip (these are different and updated from the immediately preceding PhyloGenes 3.2 release) PhyloGenes gene family trees in PhyloXML format, one file per family (e.g. <family_ID>.xml). The following information is provided for each node of a tree: 1) leaf node: branch length name <gene_id> taxonomy scientific_name sequence accession <UniProt ID> 2) non-leaf node: branch length events <duplication or speciation> 2. CSV.zip Functional information of family members in CSV format, one file per family (e.g. <family_ID>.csv). A CSV file includes the following columns: Uniprot ID Gene <Gene name. If none then Gene ID> Gene ID Gene name Organism Subfamily name The columns displayed after 'Subfamily name', if any, are GO annotations. Each column is a GO molecular function or biological process term that is annotated to at least one member of the gene family AND the annotation is supported by an experimental evidence (indicated by 'EXP') or phylogenetic inference (indicated by 'IBA'). A '0' indicates absence of either annotations.

The csv files of family members and GO annotations have been updated to include family members that were inadvertently skipped upon initial generation of all the files. Not all families were affected.