I'm trying to run an alignment of HA subtypes using ClustalOmega imported from Biopython, and I keep encountering the same error. Here's the code:
from Bio.Align.Applications import ClustalOmegaCommandline in_file = 'H1.fasta' out_file = 'H1_aligned.fasta' cline = ClustalOmegaCommandline(infile = in_file, outfile = out_file, verbose = True, auto = True) cline()
...and here's the error it generates:
ApplicationError: Command 'clustalo -i H1.fasta -o H1_aligned.fasta --auto -v' returned non-zero exit status 127, '/bin/sh: clustalo: command not found'
I've tried re-installing Biopython multiple times with no change. Any suggestions?