Aligator-to-BracketMaker Computational Pipeline The combination of Aligator and Auto-Bracket allows us to quickly build and explore CPS strategies starting only from a protein sequence. The sequence is first processed in Aligator to obtain possible segment sets, and each set (i.e., each line of Aligator's output) is converted via Auto-Bracket to a feasible ligation strategy. The final output from the process is a list of possible brackets, each representing a unique possible set of segments. We have included an "Aligator Import" tool in BracketMaker to provide a direct pipeline.