The Scipio workflow. This diagram depicts the data flow of a Scipio run. Scipio needs two FASTA files as input, one containing the protein query and one containing the genome sequence. Scipio starts BLAT and processes the BLAT results in a series of steps, successively refining and assembling the hits. Scipio's output is a YAML file, which can further be converted into a GFF file or a log file. YAML files can also be manually edited and read by a parser of which many exist for all modern programming languages. The resulting data structure can then be further processed.