How to find similarity percentage for multiple alligned sequence

Question

My question is related to protein sequence alignment. When I use ClustalW for alignmnet I can see the identity percentage, strongly similar and weekly similar. But I want to find similarity percentage of all aligned sequence not Identity.

I goggled for software's which will help to find out algorithms to solve it, but I am unable to download them ex:MStatX this sounds promising to solve my problem but somehow I can not find the information to download it.

I even read about similarity Matrix which looks like one solution to calculate the percentage similarity of the sequence. Even for this I don't know where to find information to download any software's if any exist.

Can any one please help me in finding out proper tool or method to calculate the similarity percentage in multiple aligned sequence.

Thank you, pavithra.

Answer 1

Levenshtein Distance algorithm Link to wikimedia: http://en.wikipedia.org/wiki/Levenshtein_distance You can find a implement for you specific language

Answer 2

Have you heard about Smith-Waterman? Smith-Waterman can help you to calculate the similarity of a sequence (in fact it started with the DNA..) but once you will learn how to calculate the intermediate matrix, you can use it to find many other important and useful information (such as partial matching)