Hi,
I was wondering if you would be able to tell me whether it is possible to get
the calculated conservation score (GONNET PAM250 matrix) from an alignment
produced by MSA?
>From what I understand from your literature, this is something that is
>calculated in msa by ClustalW, as it is possible to specify an arbitrary (. :
>!) identifier based on this score when performing msaPrettyPrint(). However, I
>would prefer to specify an output that gave consensus sequence with a numeric
>PAM conservation score for each residue position in the alignment. Is this
>something that I can get from the msa tool?
Thanks for your advice of this matter.
Best wishes,
Natalie
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