The new Ensembl site provides broader availability of species and genomes, but as it is in active development, not all the features from the legacy Ensembl (Ensembl 116 and Ensembl Genomes 63) versions are available. Here is a list of features profiled between the versions to help you choose which resource to use. These are valid as of July 2026.
Ensembl sites and data remain available via Ensembl Archives, please use whichever resource meets your needs best.
Key:
Features with updates and upgrades expected on new Ensembl site
Features only available on the new Ensembl site
Features that are unavailable and will not be ported over in the same format
Features with equivalent offerings across new and legacy
| Feature and data list | Ensembl 116 and Ensembl Genomes 63 | New Ensembl | Notes | Update Status |
| New genomes from projects such as DTOL, HPRC, EGP and more. | Unavailable in legacy sites | Supports the latest genome data and more genomes than ever before | New genomes are added every 2-3 weeks. Integrated releases are best for long term use. | New Ensembl only |
| Genome browsing and transcript information displays | Location and feature based views Ability to support your own tracks | Served by the Genome Browser and Entity viewer for fast visualisation | Own track support expected far into the future | Update expected |
| Sequence based displays and export functions | Highly detailed views with markup and export formats available | Sequence display for features with download option to export FASTA | New app in development for sequences | Update expected |
| Alignments view for structural variants | Unavailable in legacy sites | Available for reference human genomes and selected haplotypes | New feature only available in new Ensembl | New Ensembl only |
| Universal search with any identifier | Enabled | Limited to selected identifiers | Upgrades to search are ongoing | Update expected |
| BioMart | Available for all sites except Ensembl Bacteria | Unavailable on new Ensembl | A new data extraction tool is in development | Not available on new Ensembl |
| Ensembl Variant Effect Predictor | Fully featured web interface with plugin support for species available in legacy sites | Gene and transcript consequence only for all species including novel genomes | Upgrades to Variant Effect Predictor are part of core planning | Update expected |
| Regulatory build | Available for 10 species | Available for 10 species. Primary data can be explored in regulation.ensembl.org | Updates to regulatory annotations will be on the new Ensembl site. | Equivalent features |
| Comparative genomics features | Gene Trees, Orthology, Paralogy, Pairwise/WGA Alignment, synteny displays | Homology for genes against species in reference collections | Gene trees expected soon, more comparative features in development | Update expected |
| Archives | Available for previous data versions | Unavailable | Archives expected in Spring 2027 | Update expected |
| File downloads from FTP | Available – database dumps included | Available – serves available data | Served by different filespaces | Equivalent features |
| Ensembl REST API | Remains available for e116 for long term use | Unavailable – no plans to port over | Some tools e.g. Ensembl VEP may offer in future | Not available on new Ensembl |
| Ensembl Perl API | Remains available for e116 for long term use | Unavailable – no plans to port over | Access data via Ensembl GraphQL | Not available on new Ensembl |
| Ensembl MySQL | Remains available for e116 for long term use | Unavailable – no plans to port over | Access data via Ensembl GraphQL | Not available on new Ensembl |
| Ensembl GraphQL | Unavailable in legacy sites | Used for programmatic queries to new site data | Data is linked to genome IDs | New Ensembl only |
| Ensembl refget | Unavailable in legacy sites | Used for programmatic sequence retrieval | Use genome data from GraphQL to access sequences | New Ensembl only |
This post is specific to features and data as they were in July 2026. There will be new posts in future after the next phases of development. Please check the main page of our blog for the latest information.
For any questions or feedback, please contact the Ensembl Helpdesk.