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 Ensembl 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.
The families include all Ensembl transcripts plus the Uniprot (Swiss-Prot and TrEMBL) peptides for all the metazoans, which increases the total number of peptides represented in the gene trees.
You can view both using the gene tree, orthologues or paralogues, or protein family links from the Gene tab in the browser, or access both using the Compara API.
BioMart can be used to export homologues calculated from the gene trees.
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