How to extract SNP from MSA to create phylogenetic tree

[awalisa]

Hello,

I used Mauve program to do multiple sequence alignment (MSA) of 43 whole genome sequence and then I got ~17,000 SNP from this. Now, I have the SNP position but I do not know how can I get SNP from them. I think I would like to use concatenated SNPs to create phylogenetic tree. It maybe useful in the evolution of the different strains.

If you have any suggestion or other program which can extract SNP in multiple sequence alignment, please let's me know.

Thanks in advance,
Alisa