Software For Scores Calculation Of A Protein Multiple Alignment

Question

[vasilislenis]

Hello everybody,

I would like to ask you if you know any software that can calculate the alignment scores of a protein multiple alignment. I don't want to generate the alignment, I just want to calculate the scores in an existence alignment.

Thank you very much in advance, Vasilis.

[Neilfws]

What do you mean by "scores"? Identity, similarity? Percentages, absolute values?

[vasilislenis]

Thank you very much for your reply. I'm talking about similarity scores, like the "a" parameter in the af files

[Neilfws]

You'll have to tell us which software generates "af files." Pointing to an example would be useful.

[vasilislenis]

The maf files are been produced by MUSCLE, but why is so important the aligner that had been used? (I'm sory if my questions are so naive, but I'm really new in this field)