Substitution matrices

In this section we describe the default input $4 \times 4$ nucleotide mutation matrix $\mathbf{Q}$, $64$-entry codon usage table $\mathbf{C}$, and $20 \times 20$ amino acid substitution matrix $\mathbf{A}$. You can edit these in the files nuc.dat, codon.dat and aa.dat (respectively) if you wish, but generally you won't need to. The genetic code may be altered in the file aa2codon.dat. Further details are available from the authors or from Firth & Brown (2005, supplementary material).