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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.

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by ·Comments Off on Ensembl BioMart Sep 2026 status report

Ensembl 116 and Ensembl Genomes 63, which were released in June 2026, are the final versions of the legacy Ensembl site and services. 

We are currently in a transition phase to our new site, now available at ensembl.org, while our previous sites remain available via archives. Ensembl BioMart is one of the features that is not moving over to the new Ensembl as there is a new data mining tool in development for new site data. 

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by ·Comments Off on Service Notice: 18 Sep 2026 – Ensembl archives failing to load or loading slowly

The Ensembl archive sites are currently under heavy traffic loads causing access failures or very slow performance. We apologise for the disruption to our service and our teams are exploring solutions.

As a workaround for the Ensembl 116 Archive from June 2026 – please use the Ensembl 115 (Sep 2025) archive at https://sep2025.archive.ensembl.org/index.html 

by ·Comments Off on Updates to Phyloxml files and schema source

For Ensembl 116, we have removed the schema source link from PhyloXML files exported from Ensembl websites as the phyloxml [dot] org domain has expired.

Please take caution when using PhyloXML files from other Ensembl 116 resources (e.g. FTP site), or from Ensembl release 115 and earlier, as these contain a link to the expired schema source.

We have also updated relevant documentation on our FTP sites regarding this change.

For more details on PhyloXML we recommend the publication: Han & Zmasek (2009) https://europepmc.org/article/MED/19860910

by ·Comments Off on AlphaGenome Variant Impact scores integrated into Ensembl VEP

Following the recent launch of Google DeepMind’s AlphaGenome Atlas, the Ensembl Variant Effect Predictor (Ensembl VEP) has now integrated AlphaGenome Variant Impact (AVI) scores. This integration enables researchers to easily access AI-generated scores which estimate how likely genetic variants across the whole genome are to be deleterious. These are available to use now for human reference in the new Ensembl and the Ensembl 116 archive.

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by ·Comments Off on Ensembl is moving to our new platform this week

Ensembl is moving to our new platform for genome data and annotation this week. We will begin with the Ensembl Genomes sites and end with the Ensembl 116 site at www.ensembl.org. 

The default URL for our new site will be www.ensembl.org. This site offers new scientific opportunities, as genomes and genesets are now available for a diverse array of species from across the tree of life.

Please explore the site and the range of data available, and contact us with your needs, especially regarding new data and working with pangenome data.

There are many new features coming to the new Ensembl, along with the features you have come to love in our legacy sites. If there is a feature you need which is not yet available on the new site, the legacy sites remain available via our archives.

We have a new integrated release on our new site – 2026-07 – which integrates the latest genesets from the Ensembl 116 and Ensembl Genomes 63 releases. Read more.

We also delivered webinars on transition topics, including Educating with Ensembl, the new site, and programmatic access to genome data. Recordings are available.

Thank you for your patience over this transition period, and for joining us as we aim to share more genome data than ever before. We look forward to the insights and discoveries to come.

by ·Comments Off on The 2026-07 integrated release is now available on the new Ensembl!

This Integrated release, named “2026-07”, includes data from all partial releases on the new site up to July 2026. It serves as an interoperable dataset linking genomes across the site. This integrated release also fixes these data to this time point, making them suitable for long-term use.  

As part of the transition to the new Ensembl platform, the 2026-07 release has integrated the latest genesets from the Ensembl 116 and Ensembl Genomes 63 releases.

This is a marker release to start the transition to the new Ensembl site. We will begin updating the Ensembl URLs from 10 August through 10 September 2026.

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by ·Comments Off on Changes to URLs for the new Ensembl site

As part of our transition to the new Ensembl, we have updated the URLs for genomes on our new site. The URLs for integrated genomes now contain genome assembly accession numbers e.g. GCA_000001405.29. Some genomes on our new site contained a genome tag e.g. grch38 (examples in the post below). Saved links to these tags will now fail.

Users actively using the new site should note that any selected genome will need to be reselected after the transition of the beta.ensembl.org URL to ensembl.org. We expect this change in mid-August 2026.

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