[R] phangorn and calculation of a rate matrix

[Francisco]

Hi, I'm trying to calculate a ratematrix for a RNA aligment (U instead of T)
in order to use it as a ratematrix in Profidst (a phylogenetic program which
takes into account both the primary sequence and the secondary structure of
the RNA, in my case rRNA). The sequence-structure aligment has been made in
4SALE (a java app) and saved as one-letter encoded (using a 12 letters
alphabet, "a","c","d","e","g","h","i","k","l","n","q","r" instead of the
conventional nucleotide codes). My intention is to calculate the ratematrix
(which is a 12x12 matrix) for this special aligment with ape and phangorn,
however I've repeatdly fail to do it. The aligment is in a phyDat object
containing 30 sequences and 12 states (by using "user-defined" character
states consisting on the 12 letters indicated above). I follow the steps
described in the phangorn-specials vignette but the ratematrix (under a GTR
substitution model) is not calculated. May the problem be that phangorn only
accepts "a","g","c" and "t" as valid states for calculating the matrix? And
in case phangorn could calculate the matrix, how could I do it?
I have a very basic knowledge of R so please I would greatly appreciate (if
possible) a step-by-step explanation.
Thanks very much for the help.


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