SNP in multiple sequence alignment

[spike1985]

So it looks like no one has asked this, but how can i extract all the SNPs and positions from a long multiple sequence alignment made in clustalw. Ive got the .alm file and i dont much fancy manually going through all 200000bp of alignment.

Any ideas?

Thanks

[me_myself_andI]

Hi,

I don't think there is an easy answer to your problem. How do you define a SNP in this case? Do you have an external reference or is it part of your alignment?

And apart from that:
How many sequences do you have / how long is your alignment?
Are you sure Clustal was the right to use here in the first place?


Andreas