The TreeFam website of animal phylogenies will be retired on Wednesday 30 September, 2026. After that date, the TreeFam site will no longer be accessible and links to the site from Ensembl 115 and earlier will no longer function.

TreeFam databases and data files are available at the TreeFam FTP archive: https://ftp.ebi.ac.uk/pub/archive/treefam/

The decision to retire TreeFam in 2026 was necessary because the most recent update (release 9) was published in 2013. As such, the current TreeFam website has not seen a major update in more than a decade and the burden of technical debt has made it increasingly difficult to maintain the site.

Two decades have passed since the TreeFam website of animal gene phylogenies first went live, following an international collaborative effort (Li et al. 2006).

During that time, successful collaboration between TreeFam and Ensembl Compara (Ruan et al. 2008; Schreiber et al. 2013) shaped the methods of both resources. 

We are actively working to bring some of the functionality of TreeFam into Ensembl and will update users as this progresses.

If you have any questions about the TreeFam resource, contact us via the EMBL-EBI support form: https://www.ebi.ac.uk/about/contact/support/ and include TreeFam in the request subject. 

Authored by: Thomas Walsh

Reviewed by: Jitender Cheema, Jorge Batista da Rocha and Emily Clark