Hi so I have a snp alignment and I would like to use some software to classify all of my samples into a group eg 0 or 1 depending on whether they have the wild type or mutant base at any given variable site.

eg

sample 1 (wild type)
actga

Sample 2 (query)
accgg

so sample 2 would be eg. 0 at position 1 and 1 and position 3. The reason I want to do this is so that I can characterise snps which are 'lineage determining'