search for: phydat

Hello, I'm struggling with understanding the output on the ancestral.pars() command from the phangorn package, I'm new to doing phylogenetic analyses using R. I used it on nucleotide data, and it works fine, I'm just not sure how to read the output. The output is phyDat class, and outputs a matrix for each node/leaf in the tree. I figured out that the matrix columns represent the four nucleotide states a, c, g, t, but what I'm unclear about is what the rows represent, and what do the row names mean, the seem to be powers of 2, (1,2,4,8) etc, do these represent...

...,"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 th...