how to write a Perl Program to find out SNPs from a given multiple sequence alignment.
I don't think asking anyone to write an entire program for your needs, and even without any kind of description of the problem, is the best thing to do at any forum. who knows, you may be luckier if you spend some time at least describing the input and the desired output.
It would have been better if you atleast demand for some lines of script instead of whole program. If you provide more description about your need then Biostar people are definitely helpful.
What you are asking for is generally referred to as 'SNP calling'. There is a Biostar question about it.
If you want a software to do it, just search for 'SNP calling tools' or 'SNP calling from multiple alignment' on google. Note how the latter query gets you to tools like PineSAP that seems to have been developed to solve your problem.
i was asking for the concept. And i have got the answer. It is using optimal mismatching algorithm.
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