Figure 1
From: A model-independent approach to infer hierarchical codon substitution dynamics
Three levels of dynamics by Markov chain lumping. (a) Codon substitutions are modeled as a Markov chain. States represent codons and transitions represent substitutions between codons. (b) If the codons are aggregated with respect to the amino acids they code for, the new aggregated process remains a Markov chain. For instance, since AAA and AAG both code for lysine, they can be aggregated into one unit. (c) Specific aggregates of amino acids also exist such that their dynamics is Markovian. Lysine and arginine can for example be merged to form one state.