The Bird 10K 363-way alignment is available as two tracks: a MAF format track (using a bigMaf file), only available on the Gallus_gallus (chicken) browser, as well as snake tracks (using a HAL(Hickey et al. 2013) file) that are available on all genomes.
Note that the snake tracks need to load much more data and are thus significantly slower to load than the MAF tracks. We suggest using no more than five snake tracks at a time, and viewing them in regions of 100kb or less to avoid browser timeouts.
The Bird 10K consortium has released 268 newly sequenced avian genomes. These were combined with other publicly available genomes to create a set of 363 bird genomes used for the alignment. These genomes were aligned using Cactus, a multiple whole-genome alignment program(Paten et al. 2011).
The raw alignment (in HAL(Hickey et al. 2013) format) is available here. Please be aware that the file is hundreds of gigabytes in size, and bandwidth costs for hosting this file are significant.
The Bird 10K consortium provided the assemblies and generated the alignment. Please contact the corresponding authors for the data release, Guojie Zhang and Benedict Paten with questions.
Hickey, G., B. Paten, D. Earl, D. Zerbino, and D. Haussler. 2013. “HAL: a hierarchical format for storing and analyzing multiple genome alignments.” Bioinformatics 29 (10): 1341–2. https://doi.org/10.1093/bioinformatics/btt128.
Paten, B., D. Earl, N. Nguyen, M. Diekhans, D. Zerbino, and D. Haussler. 2011. “Cactus: Algorithms for genome multiple sequence alignment.” Genome Res. 21 (9): 1512–28.