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Species trees

The Compara pipelines use two main species trees.

  1. The NCBI taxonomy (i.e. topology only) in:
    • the Protein-trees pipeline
    • the ncRNA-trees pipeline, where the three sub-trees Eutheria, Sauria, and Clupeocephala are flattened
    • the CAFE pipelines (Gene Gain/Loss trees), with branch lengths coming from the TimeTree database
  2. A tree with branch-lengths computed in-house with Mash (available for download here) in: