Multiple alignments pipeline. Colours and conventions are used as in Figure 3. (A). This pipeline can be divided in 4 blocks. In the first part there is one job per species, which prepares all of the BLAST jobs. The second part (one job per coding exon) runs the BLAST jobs. In the third part, Mercator builds the orthology map using all the previous BLAST results. In the last part, each Mercator block is aligned with Pecan and GERP defines the local conservation in each alignment. In this pipeline, the SubmitPep_X_Species and blast_X_Species analyses are created dynamically by the GenomeSubmitPep and GenomeDumpFasta jobs respectively. GenomeLoadExonMembers (1 job per species) loads all the coding exons and create 1 GenomeSubmitPep and 1 GenomeDumpFasta job for each genome. The GenomeSubmitPep analysis creates 1 SubmitPep_X_Species analysis per genome and all the jobs for each of these analyses. GenomeDumpFasta creates a BLAST database for each set of coding exons and the corresponding blast_X_Species analysis. CreateBlastRules creates all the dataflow rules between the SubmitPep_X_Species and the blast_X_Species for all the other species. Mercator builds the orthology map using the results of all the previous BLAST jobs and then Pecan aligns all the orthologous genomic segments in each Mercator block. Last, the Gerp is run on each Pecan alignment. (B) Timeline for the 12-way Multiple alignment pipeline.