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What is the amino acid states order in a Hyphy matrix 20x20? (Read 3323 times)

Miguel

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Hi Hyphy!

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What is the amino acid states order in a Hyphy matrix 20x20?
Apr 27^th, 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

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Sergei

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Datamonkeys are forever...

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Re: What is the amino acid states order in a Hyphy matrix 20x20?
Reply #1 - Apr 27^th, 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");

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

Sergei

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Division of Infectious Diseases
Division of Biomedical Informatics
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University of California San Diego

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Miguel

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Hi Hyphy!

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CBMSO, CSIC (Spain)
Gender: male

Re: What is the amino acid states order in a Hyphy matrix 20x20?
Reply #2 - Apr 28^th, 2014 at 5:44pm

Hi Sergei,

Thanks!
So, do you mean something like?
Code:

chars = "ACDEFGHIKLMNPQRSTVWY";
GetDataInfo (chars, filteredData, "CHARACTERS");

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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