A snp caller from a multiple alignment using python/biopython

Question

[cnyaigoti]

Hi,

I want to call all nucleotide SNP positions from a virus genome multiple sequence alignment of about 15000 nucleotides long. Any one done this? I will prefer to use python I will like the script to return an output of the number of SNP positions detected, actual position in the original alignment and the alignment column the SNP was detected. Gaps to be ignored.

I will appreciate,

Charles

[Devon Ryan]

Why not just use a premade tool? A quick google for "virus ngs variant call" will yield some useful results.