Whole genome alignments for mammals, fish, insects, grasses, cereals and more are now available via a central repository: https://ftp.ensembl.org/pub/misc/compara/multi/hal_files/
Continue readingTag: comparative genomics
TreeFam website will be retired soon
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.
Continue readingLarge plant protein clusters accessible via gene families view
In Ensembl release 116 (Ensembl Genomes 63), two large protein clusters in Plants have incomplete or missing homology data due to production constraints. To address this, we set about making these clusters accessible via the gene families view. Please read on if you’d like to know more about these clusters, both associated with the Panther subfamily ‘PTHR11439_SF127’.
Continue readingChanges to default track visibility in selected Cactus alignment image views
Gene and Sequence tracks in Genomic Alignment Images for selected Cactus alignments will be hidden from view at medium and large scales in Ensembl Release 114.
Continue readingExpanding Ensembl Metazoa gene trees
As of Ensembl 110 / Ensembl Genomes 57, gene trees within Ensembl Metazoa have been expanded to cover 275 species by dividing them into 3 taxonomic clade sets: Metazoa, Protostomia, and Insecta. In addition, the release and update frequency of metazoan gene trees will change, with Metazoa and Protostomia being updated in every even-numbered release and Insecta being updated in every odd-numbered release. Read on to find out more about this update.
Continue readingChanges to endpoints of Ensembl Compara APIs in release 110
We have made a number of changes in Ensembl Compara Perl API and REST API endpoints. These changes allow Ensembl to handle non-unique member stable IDs when retrieving comparative genomics data via the APIs. These changes will come into effect in Ensembl release 110 and all old endpoints will be retired in release 112. Please continue reading if you regularly retrieve comparative genomics data via the Ensembl APIs.
Continue readingFree Ensembl Browser and REST API virtual workshops in November
Virtual series covering the genome browser and the REST API. Both workshops will be held between Tuesday – Thursday, with the Browser on 15th – 17th November and the REST API on 22nd – 24th November 2022 (9am-12pm GMT). Read on for more information and registration instructions.
Continue readingGetting to know us: Ivana from Ensembl Compara
This month, we meet Ivana Piližota, who joined the Ensembl Compara team in 2020. She tells us how her everyday work life looks like and what sparked her interest in bioinformatics.
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