(I work at Benchling and worked on the protein alignments tool.) Adding to Vineet's response, Benchling has both CRISPR search and sequence alignment, and they

(I work at Benchling and worked on the protein alignments tool.) Adding to Vineet's response, Benchling has both CRISPR search and sequence alignment, and they have different use cases. CRISPR search uses the custom algorithm described in the article (and the "last post" linked at the top), while alignments use the two popular alignment tools Clustal Omega[1] and MAFFT[2]. It's certainly true that the general alignment problem is complex had has undergone plenty of research around performance and producing good results, which is why we used an off-the-shelf tool for computing the alignment itself (but a custom UI for viewing the result). [1] http://www.clustal.org/omega/ http://www.clustal.org/omega/ [2] https://mafft.cbrc.jp/alignment/software/ https://mafft.cbrc.jp/alignment/software/