More information about the file formats can be found: - OrthoXML at http://orthoxml.org - PhyloXML at http://www.phyloxml.org This directory contains all the XML dumps of the gene-tree related resources: - the gene trees themselves - the orthologies, which are derived from the gene trees - the CAFE trees, which analyze the expansion and contraction of gene families Compara.{release}.{protein|ncrna}_{species_collection}.allhomologies.orthoxml.xml.gz Contains all the orthologies in a single OrthoXML file. Each orthology is stored as an orthologGroup containing two genes. Compara.{release}.{protein|ncrna}_{species_collection}.allhomologies_strict.orthoxml.xml.gz Contains all the "strict" orthologies in a single OrthoXML file. Each orthology is stored as an orthologGroup containing two genes. In this file, all the homologies are fully compliant with the species tree. Compara.{release}.{protein|ncrna}_{species_collection}.alltrees.orthoxml.xml.gz Contains all the trees in a single OrthoXML file. All the trees are attached to the root 'groups' tag. The following three files are tar archives containing tar archives, containing one file per tree, so that each tar file doesn't contain more than 500 files. Compara.{release}.{protein|ncrna}_{species_collection}.tree.orthoxml.tar Each file will contain one tree, in OrthoXML format. Compara.{release}.{protein|ncrna}_{species_collection}.tree.phyloxml.tar Each file will contain one tree, in PhyloXML format. Compara.{release}.{protein|ncrna}_{species_collection}.tree.cafe_phyloxml.tar Each file will contain one CAFE tree, in PhyloXML format.