clustering based on SNP information

[strob]

Dear all,

I have re-sequencing data for many genotypes for the same set of genes. As expected, the differences are minor and are most of the time SNPs. As I want to cluster the genotypes based on their SNP appearances/comparisons, I wonder if there's a tool out there which can do this?
A tree kind of structure would be a really nice outcome.

Many thanks for the help,

Steven

[Oxygen81]

Hello Steven,
can you extract the SNPs into a list (MS Excel) with the columns: some ID, Position compared to a reference (use always the same reference), the base in the reference and the SNP. I could generate you an "alignment" what you can use with every evolutionary reconstruction program.
Janina