I would like a list of homologues to my gene. Should I look at the gene trees or the families?
Although there is overlap, the EnsemblCompara MCL Families and Gene Trees are two different complementary data sets.
To construct the Gene Trees, only the longest translation of each gene is included, and only species represented in Ensembl are used. However, the methodology has been specifically constructed to find homology relationships.
The families include all Ensembl transcripts plus the Uniprot (Swiss-Prot and TrEMBL) peptides for all the metazoans, which duplicates the total number of peptides represented in the gene trees. These families are clustered using a Markov Clustering method, MCL.
BioMart can be used to export homologues calculated from the gene trees.