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 (available for download here) in:
   • the Multiple-alignment pipelines
   • the Constrained Elements / Conservation Scores pipelines
   We pass the unmasked whole genome sequences to Mash to compute pairwise distances, and then we generate the species tree using distance-based neighbour-joining guided by taxonomy.