**70**wrote:

Hello,

I have a file with protein sequences for which I would like to know the **similarity score** of the **multiple sequence alignment**.

I have aligned these sequences using ClustalW, but all I get is the pairwise identity score !

I am not looking for the pairwise identity or similarity score, but the similarity score of the multiple sequence alignment, so that I can conclude that "**this group of sequences are x% similar with each other**".

Is there any tool that gives a **measure of similarity of the sequences** ? Or any method for **calculating this score** ?

Please help !

Thank you, Ananth

the similarity score depends on the substitution matrix used. So you should never say "this group of sequences are x% similar with each other" but rather "this group of sequences are x% similar with each other given this specific substitution matrix". Moreover, check you are doing a global alignment and not a local one.

26kThank you Giovanni,

As you correctly pointed out, yes for a specific substitution matrix in a global alignment is there a way to calculate this similarity score for a MSA ?!

70