FsePSA is a tool that is based on a new scoring scheme with an algorithm for the pairwise alignment of Coding DNA Sequence(CDS) accounting for frameshift translation initiation and length, while simultaneously considering nucleotide and amino acid sequences. The main specificity of the scoring scheme is the introduction of a penalty cost accounting for frameshift extension length to compute an adequate similarity score for a Coding DNA Sequence(CDS) alignment. The second specificity of the model is that the search space of the problem solved is the set of all feasible alignments between two Coding DNA Sequence (CDS).
Jammali, S., Kuitche, E., Rachati, A., Bélanger, F., Scott, M., & Ouangraoua, A. (2017). Aligning coding sequences with frameshift extension penalties. Algorithms for Molecular Biology, 12(1), 10.