variant calling using SeqIO

[ksw9]

Hi, I am new to Python and am trying to write a simple script to loop over sites in a multiple fasta file to identify variant sites. I would like to loop over each residue and then as an output, (1) have a list of variant positions, (2) concatenate residues at SNP sites for each sample (construct a list of haplotypes). Could you point me towards code that allows me to loop over residues in a multiple alignment?

Thank you!

[maubp]

It sounds like you want to align the sequences (eg with Clustal or Muscle), then you can load the multiple sequence alignment with Biopython's Bio.AlignIO.read(...) function, and look at each column.

[ksw9]

Yes, perfect thank you!