OrthoDB 11

Files from OrthoDB v.12 are available at https://bioinf.uni-greifswald.de/bioinf/partitioned_odb12/.

We here provide clade-partioned files generated from OrthoDB v.11 for usage with BRAKER2 and BRAKER3. When using this data, please cite:

Kuznetsov, D., Tegenfeldt, F., Manni, M., Seppey, M., Berkeley, M., Kriventseva, E. V., & Zdobnov, E. M. (2023). OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity. Nucleic Acids Research, 51(D1), D445-D451.

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 (4.6 GB, md5sum: a0e6ff3fe2061cc7a9027616691e6060)
  • Vertebrata.fa.gz (3.1 GB, md5sum: 27bf52491da63469edc6b323be51bda1)
  • Viridiplantae.fa.gz (1.3 GB, md5sum: 59bd04dd98102b8cd51b1d0d8d993105)
  • Arthropoda.fa.gz (1.2 GB, md5sum: 7aa03dbcef38517752be16004ad9cb76)
  • Eukaryota.fa.gz (8.5 GB, md5sum: ff74dbac56700926b9acc39e17ce323a)
  • Fungi.fa.gz (2.2 GB, md5sum: 3cd9cb99d70730093f3f64ebe2f15f9b)
  • Alveolata.fa.gz (201 MB, md5sum: 1c38818489a598843e985e73b45c0ade)
  • Stramenopiles.fa.gz (108 MB, md5sum: eab4b468d1fcc91c8477d04c797e37aa, should be combined with proteins from another clade for BRAKER, or use Eukaryota.fa.gz)
  • Amoebozoa.fa.gz (38 MB, md5sum: fa094c9d01fb6bafd5dfa701b1f4efaf, should be combined with proteins from another clade for BRAKER, or use Eukaryota.fa.gz)
  • Euglenozoa.fa.gz (99 MB, md5sum: 5cb75b7d80b953e1d326b4f863ed6739, should be combined with proteins from another clade for BRAKER, or use Eukaryota.fa.gz)

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.