Align a single fasta file containing two DNA sequences using local alignment. from Bio.Emboss.Applications import NeedleCommandLine needle_cline = NeedleCommandline() needle_cline.asequence="data/alpha.faa" needle_cline.bsequence="data/beta.faa" needle_cline.gapopen=10 needle_cline.gapextend=0.5 needle_cline.outfile="needle.txt" print(needle_cline)

print(needle_cline.outfile)