PELOPS is an effort to identify biologically functional sub-sequence similarities among related sequences that do not align using traditional methods (e.g. BLAST) because the conservation allows for some rearrangement. Sequences that fit such a description include promoters and introns, which may contain clusters of binding sites, sometimes swapping positions or strands.
Unlike motif-finders, which aim to discover an optimal position weight matrix among multiple sequences, PELOPS is a pairwise similarity method.
Bioinformatics programs are often acronyms. PELOPS is short for Pairwise Evaluation Local Of Punctate Similarities. This reads better when you swap the middle words: "pairwise evaluation of local punctate similarities". Apparently, whoever made up the acronym, didn't assemble it perfectly.
Sometimes, there's more to a name than an acronym. In Greek mythology, Pelops was a son of Tantalus, who cut his son into pieces, placed him in a stew, and served him for dinner. The gods were not amused, and Pelops was reassembled from his pieces, minus his shoulder. Whether it's Greek gods, acronyms, or biological subsequences, sometimes perfection is out of reach.
pelops is designed as a single-file application with multiple functions. All
of the libraries are vanilla Python: there are no external dependencies to
manage.