The GeneTree pipeline. Colours and conventions are used as in Figure 3. (A) The figure shows only the second half of the pipeline as the first part is very similar to the first two blocks of the Multiple alignment pipeline (panel 4A). The main difference is that we use the BLAST between the whole proteins as a block instead of splitting them in coding exons. In short, the proteins are clustered and aligned and a phylogenetic tree is built on top of each alignment. Then, the OrthoTree module calls orthologues and paralogues and the last 3 modules handle the calculation of dN/dS values for pairs of proteins. This pipeline contains alternative routes depicted in turquoise used when some particular exceptions are thrown, namely when Muscle is unable to align all the proteins in a cluster or when TreeBeST cannot infer the phylogenetic tree. This can happen when the cluster of proteins is too large. We use the BreakPAFCluster module to split these clusters in sub-groups and restart the alignment. (B) Timeline for the GeneTree pipeline. This figure shows the progress of the GeneTree pipeline for Ensembl release 49 (39 species). The pipeline is monitored approximately every 2 minutes. BLAST and SubmitPep jobs co-occur in one phase of the pipeline. In another phase, Muscle, TreeBeST and OrthoTree also run at the same time.