As well as providing alignments of genome sequence, the Ensembl comparative genome analysis pipelines also generate gene trees and orthology/paralogy prediction across all Ensembl genomes. A full description of the pipeline including its close collaboration between the curated resource Treefam (31) is forthcoming (Vilella, A. et. al., submitted). A significant recent change (release 50) has been the calculation of site-wise dN/dS values in our gene trees using the SLR programme (sitewise likelihood ratio estimation of selection) (32). These values allow us to detect positions in the alignments that are under different evolutionary pressure.
