This repo is a direct clone of James-S-Santangelo/Degeneracy (cloned from tvkent/Degeneracy) with a few minor modifications to enable the Great tit (Parus major) genome and annotation file to be used as inputs. This pipeline also include the modifications made by James S. Santangelo for get_4fold_sites.sh to accept command-line arguments in the following order: gff, fasta, outpath.