[Bioc-devel] MSA Consensus

Natalie Stephenson N.L.Stephenson at leeds.ac.uk
Mon Mar 13 18:36:22 CET 2017


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,

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