x3 — Rate matrix on triplets/codons constructed from nucleotide rates

Construct a triplet or codon rate matrix from a nucleotide rate matrix.

Stationary inputs produce stationary models. For stationary non-reversible inputs, equilibrium frequencies are recalculated from the constructed rates.

For non-equilibrium inputs, root frequencies are calculated by multiplying the nucleotide frequencies at the three positions, then normalizing over the allowed triplets or codons.