pip install biopython python from Bio import pairwise2 from Bio.Seq import Seq seq1 = Seq("ATTGCCATTGCGC") seq2 = Seq("ATGGCCATTAGCGCA") alignments = pairwise2.align.globalxx(seq1, seq2) for alignment in alignments: print("Score: ", alignment.score) print("Seq1: ", alignment.seqA) print("Seq2: ", alignment.seqB) - Biopython Tutorial and Cookbook: http://biopython.org/DIST/docs/tutorial/Tutorial.html - Biopython Documentation: http://biopython.org/DIST/docs/api/