Sorry if this is really obvious, i'm really new to Bioinformatics. I have a list of alleles from MHC2, all with accession numbers (theres 18) I downloaded the FASTA sequences for these and did a multiple alignment of them using ClustalX. I now need to generate a database of SNPs for each one and add frequencies etc, and I am a little confused on how to do this. I can see differences in the alignments but not everyone of these differences would necessarily be a SNP right? Is there a program that will take the alignment data and give me a list of SNPs for each allele or is there another way I could be doing this?