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HYPHY Package >> HyPhy feedback >> What is the amino acid states order in a Hyphy matrix 20x20?
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Message started by Miguel on Apr 27th, 2014 at 7:49am

Title: What is the amino acid states order in a Hyphy matrix 20x20?
Post by Miguel on Apr 27th, 2014 at 7:49am
Hi There,

This is a very easy question. I am wondering what is the amino acid order in the 20x20 matrices of Hyphy (i.e., WAG.mdl), I mean to which amino acid state belongs each number?. For example, ModelMatrixName[0][0] "might" correspond to A -> A, but what is the list of the corresponding states for all numbers 0 - 19?

Many thanks!  :)

Best,
Miguel

Title: Re: What is the amino acid states order in a Hyphy matrix 20x20?
Post by Sergei on Apr 27th, 2014 at 9:00am
Hi Miguel,

The model itself does not assign any characters to the indices; the mapping happens at the level of a data filter -- the same 20-state model can produce arbitrary sets of 20 characters. The default amino-acid mapping is alphabetical, i.e. ACDEFGHIKLMNPQRSTVWY; this is what amino-acid filters read from alignment files adhere to.

You can use, for example,

[code]
     GetDataInfo (chars, filter, "CHARACTERS");
[/code]

to store the 0:N-1 character mapping of the N-state "filter" in the "chars" variable.

Sergei

Title: Re: What is the amino acid states order in a Hyphy matrix 20x20?
Post by Miguel on Apr 28th, 2014 at 5:44pm
Hi Sergei,

Thanks!
So, do you mean something like?
[code]
chars = "ACDEFGHIKLMNPQRSTVWY";
GetDataInfo (chars, filteredData, "CHARACTERS");
[/code]

Anyway, given by default it is the alphabetic order, if I just give the values in the matrix according to such an order I guess I do not need to use "GetDataInfo", correct?

Thanks again!  :)
B,
Miguel

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