pip install biopython python from Bio import SeqIO from Bio import pairwise2 seq1 = SeqIO.read("seq1.fasta", "fasta") seq2 = SeqIO.read("seq2.fasta", "fasta") alignments = pairwise2.align.globalxx(seq1.seq, seq2.seq, one_alignment_only=True) for alignment in alignments: print(alignment)