D. melanogaster proteins annotated by FlyBase were aligned against the
D. simulans genome assembly using Spaln2 with cross-species parameters.
D. melanogaster proteins were mapped against the D. simulans
genome assembly with tblastn. For each protein, the region surrounding
the best tblastn hit is identified and each protein is re-aligned against this
genomic region with Spaln2 using cross-species parameters optimized for
D. melanogaster: (-Tdromel -yX).