Substitution rates in genes can provide information about their evolutionary dynamics and divergence among either species or protein groups. This work presents PANAS, a computational pipeline developed to facilitate the obtention of substitution rates in large amounts of genomic data from different taxa. We tested PANAS by analyzing the evolution of the mitochondrial protein-coding genes (PCGs) from 18 species of platyhelminths. Our results suggest that the cox1, cox2, cytb, and nad1 genes are under strong selection pressure at the nucleotide and protein level in platyhelminths.