November 2023 Nature Zoonomia with expanded primates alignment

November 2023 Nature Zoonomia with expanded primates alignment

This is the alignment used in the following paper, where the primates clade of the 241-way Zoonomia mammals alignment was expanded to include more primates, resulting in a 447-way alignment:

• Kuderna, L.F.K., Ulirsch, J.C., Rashid, S. et al. Identification of constrained sequence elements across 239 primate genomes. Nature (2023). https://doi.org/10.1038/s41586-023-06798-8

The resources for this paper are:

• 447-way mammalian alignment (Zoonomia + new primates)
  • All steps to reproduce:
    • https://cgl.gi.ucsc.edu/data/cactus/447-mammalian-2022v1.README.md
  • HAL alignment (1.2 terabytes)
    • URL: https://cgl.gi.ucsc.edu/data/cactus/447-mammalian-2022v1.hal
    • MD5: 3a9dbc922f36b149d89d2c6a60244832
    • Newick tree: https://cgl.gi.ucsc.edu/data/cactus/447-mammalian-2022v1.nh
  • MAF Alignment (779 gigabytes), human reference (Updated Nov 10, 2025, to fix MAF formatting bug)
    • URL: https://cgl.gi.ucsc.edu/data/cactus/447-mammalian-2022v1.fix2.single.maf.gz
    • MD5: 5af994162b24790d29189c492a99c39f
    • Index: https://cgl.gi.ucsc.edu/data/cactus/447-mammalian-2022v1.fix2.single.maf.gz.tai
    • Log: https://cgl.gi.ucsc.edu/data/cactus/447-mammalian-2022v1.fix2.maf.gz.log.gz
  • MAF Alignment with Duplications (1.1 terabytes), human reference (Updated Nov 10, 2025, to fix MAF formatting bug)
    • URL: https://cgl.gi.ucsc.edu/data/cactus/447-mammalian-2022v1.fix2.maf.gz
    • MD5: fc8849ff2a4dffc23e2d27c613e33e6a
    • Index: https://cgl.gi.ucsc.edu/data/cactus/447-mammalian-2022v1.fix2.maf.gz.tai
    • Log: https://cgl.gi.ucsc.edu/data/cactus/447-mammalian-2022v1.fix2.maf.gz.log.gz
    • Note: This MAF can contain multiple rows per block for the same species

Contacts

Benedict Paten
Mark Diekhans