Hi

My data consists of sequences that have a 0 or 1 indicator before each codon. For example, 0ACT1GAG.

I use $BASESET:"ACGT01" in my data file and exclude the attached "exclusions.txt" combinations in my filter. These exclusions are any combination of length four of A, C, G, T, 0 and 1 which does not have a 0 or 1 indicator in the first position and 3 nucleotides in the following three positions. It also contains the stop codons, six in total (0TAA,0TAG,0TGA and 1TAA,1TAG,1TGA).

The rate matrix (122 x 122) I specify for the model assumes the indices are coded as follows:
0 = 0AAA
1 = 0AAC
61 = 1AAA
121 = 1TTT

Is this consistent with how HyPhy expects it?

Thanks