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The Avianbase Project is an initiative led by the Roslin Institute in collaboration with the Avian Phylogenomics Consortium and Ensembl to make the initial sequence and annotation available for 44 bird species within the Ensembl framework.

All genomes

View full list of all species from the Avian Genome Consortium

Original Ensembl annotations for vertebrate and other species are available in Ensembl, in Ensembl Pre! and in EnsemblGenomes

The Avianbase Project

The Avianbase Project is using the Ensembl infrastructure to share data brought together by the Avian Phylogenomics Consortium (as part of the Avian Genome Consortium) for 44 birds. The genome sequences, except for budgerigar and bald eagle, were sequenced by the BGI. Genome annotations were also generated by BGI using GeneWise based on a selection of Ensembl transcripts for chicken, zebra finch and human. Further informations on the data/annotation can be found in the papers referenced below.


The data types and sources made available here are as follows:

  • Genome sequences - generated by BGI
  • Gene annotations (gene, transcript and peptide information) - generated by BGI
  • Repeat annotations (dustmasker, tandem repeat finder, RepeatMasker and RepeatModeler) - generated at the Roslin Institute


  1. Eöry L, Gilbert MT, Li C, Li B, Archibald A, Aken BL, Zhang G, Jarvis E, Flicek P, Burt DW: Avianbase: a community resource for bird genomics. Genome Biology 2015, 16:21.
  2. Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, Fonseca RR da, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, et al.: Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 2014, 346:1320–1331.
  3. Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, et al.: Comparative genomics reveals insights into avian genome evolution and adaptation. Science 2014, 346:1311–1320.
  4. Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Alfaro-Núñez A, Narula N, Liu L, Burt D, Ellegren H, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MTP, Zhang G, and The Avian Phylogenomics Consortium. Phylogenomic analyses data of the avian phylogenomics project. GigaScience. (2014) http://dx.doi.org/10.5524/101041
  5. Zhang G, Li B, Li C, Gilbert MPT, Jarvis ED, Wang J, The Avian Genome Consortium: Comparative Genomic Data of the Avian Phylogenomics Project. GigaScience (2013) DOI: 10.1186/2047-217X-3-26