OrthoDB 12

Files from OrthoDB v.11 are still available at https://bioinf.uni-greifswald.de/bioinf/partitioned_odb11/.

We here provide clade-partioned files generated from OrthoDB v.12 for usage with BRAKER2 and BRAKER3. When using this data, please cite:

Fredrik Tegenfeldt, Dmitry Kuznetsov, Mosè Manni, Matthew Berkeley, Evgeny M Zdobnov, Evgenia V Kriventseva, OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes, Nucleic Acids Research, 2024; gkae987, https://doi.org/10.1093/nar/gkae987.

OrthoDB is officially maintained and hosted at https://www.orthodb.org/ by the group of Prof. Zdobnov. OrthoDB data is under the Creative Commons Attribution License. We kindly thank Evgeny Zdobnov and his team for supporting our genome annotation projects by providing this excellent data set.

The following partitions are available for download:

  • Metazoa.fa.gz (12 GB, md5sum: b594d3044921ede2680eb65526dae662)
  • Vertebrata.fa.gz (5.8 GB, md5sum: f91cbc7da91ce64c3c3278357e41e836)
  • Viridiplantae.fa.gz (3.0 GB, md5sum: 34c1f027a1a7b10f225b69fbd5500587)
  • Arthropoda.fa.gz (4.4 GB, md5sum: 02c9a5cc4efb9d4d5957f6bd2017a03a)
  • Fungi.fa.gz (7.2 GB, md5sum: df3a892610c115dc1459bea6666809fc)
  • Alveolata.fa.gz (444 MB, md5sum: 96eb7cbce73db770c0c6b071b4b790a4)
  • Stramenopiles.fa.gz (343 MB, md5sum: 865c11dd3d538db46a54a7b0f2f17f66, should be combined with proteins from another clade for BRAKER, or use Eukaryota.fa.gz)
  • Amoebozoa.fa.gz (48 MB, md5sum: 1c2a52daa3637f4a3ef085adb26559e1, should be combined with proteins from another clade for BRAKER, or use Eukaryota.fa.gz)
  • Euglenozoa.fa.gz (106 MB, md5sum: a64bfecfa1b33aee24ffe543368d26ee, should be combined with proteins from another clade for BRAKER, or use Eukaryota.fa.gz)

If none of the above listed partitions satisfies your needs, we also provide the larger Eukaryota.fa.gz (23 GB, md5sum: f356006a608f30e413cfcf1ab55698cb).

You need to unzip the files with "gunzip *.fa.gz" prior using them for genome annotation pipelines maintained by the team in Greifswald.

These partitioned OrthoDB files were prepared using software by Tomas Bruna: https://github.com/tomasbruna/orthodb-clades.