More information about the file formats can be found:
 - OrthoXML at https://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.

