HyPhy message board | |
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl
HYPHY Package >> HyPhy feedback >> What is the amino acid states order in a Hyphy matrix 20x20? http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1398610169 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 |
HyPhy message board » Powered by YaBB 2.5.2! YaBB Forum Software © 2000-2024. All Rights Reserved. |