I am having an issue with my biopython program. My project is due soon and I can't figure out what's going on.
I am running this code based on a tutorial, and I'm new to python. Here is my code:
from Bio import SeqIO from Bio.Align.Applications import ClustalOmegaCommandline clustalomega_cline = ClustalOmegaCommandline(infile="hla.fasta", outfile="alignment.aln", verbose=True, auto=True)
This gives a command that I can run and create the alignment. This works fine.
The issue here is that, from my research, I've read that Clustal Omega outputs information on which portions of the sequences are conserved and variable based on symbols (like "*" and ":", etc). My output file is just in fasta format, even though I specified "aln".
What am I doing wrong?
Here is some of the alignment.aln file: