Have a look at http://bioperl.org. Also, we are not biologists and thus "sequence similarity" and "consensus sequence" tell us very little. You will have to provide more technical explanations how you would measure similarity and what "consensus" would mean in your case. Also see what has to offer for FASTA.

Please note that this site is not a script writing service. While we will assist you with writing your code, we expect you to do the majority of the work and show some effort. This mostly involves you showing the code you have already written and explaining where you encounter the problem.