by ·Comments Off on Retirement of species name based structure on the new Ensembl FTP 

The species name based structure on the new Ensembl FTP space (https://ftp.ebi.ac.uk/pub/ensemblorganisms/) will be retired within the next two weeks.

Files for all previously released genomes remain accessible in the new structure under the GCA or GCF subdirectories e.g.  https://ftp.ebi.ac.uk/pub/ensemblorganisms/GCA/000/001/405/29 

To assist with search, we provide a JSON manifest file which lists genome annotation data and its location.

More information on the structure and filetypes is available in our FTP download documentation. 

by ·Comments Off on Ensembl archives from 2015 and earlier will be retired soon

Ensembl hosts four archives which represent milestones for the older versions of assemblies for popular species.

The following sites and their tools, including BioMart access will no longer be available.

  • Ensembl 80: May 2015 – https://may2015.archive.ensembl.org/ -Annotation on the mouse GRCm38 assembly
  • Ensembl 77: Oct 2014 – https://oct2014.archive.ensembl.org/ – Annotation on the zebrafish Zv9 assembly
  • Ensembl 75: Feb 2014 – https://feb2014.archive.ensembl.org/ -Annotation on the human GRCh37 assembly
  • Ensembl 54: May 2009 – https://may2009.archive.ensembl.org/ -Annotation on the human NCBI36 assembly, zebrafish Zv8 assembly

Ensembl data files for these archives remains available via FTP:

For any questions or concerns please contact the Ensembl Helpdesk.

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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.