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closeQuestion about "strange" replacement scores
Posted by fabascal on 26 Jun 2007 at 13:39 GMT
Estimated colleagues,
I noticed that scores in the "within" and "between" HIV matrices (available at: http://www.hyphy.org/pubs...) are "strange". For instance, the replacement betwen the amino acids Tryptophan (W) and Aspartic acid (D) has a score of 0, 2 or 3 in "Between10%", "Between38%" and "Within5%" matrices, respectively. This is strange because W is usually the least mutable amino acid (no other has similar physicochemical properties), and also because W and D are VERY different amino acids.
I wish to thank you for this interesting analysis.
Federico Abascal
RE: Question about "strange" replacement scores
fabascal replied to fabascal on 26 Jun 2007 at 13:56 GMT
just to add that it seems that this problem only affects to the "supplementary" data provided at http://www.hyphy.org/pubs... but not for instance to the matrix plots shown in figure 1.
Federico Abascal