Figure 1. An outline of the Codonevo simulations.
A. Population dynamics. During each cycle a population of coding systems undergo two stages, birth (where a number of coding system copies are created according to a replication function ρ) and death (where coding systems are randomly destroyed until their number reaches a certain constant limit O). B. Obtaining the replication function ρ for each coding system. A coding system consists of a single mRNA sequence and a set of tRNA rules that are used to produce a protein sequence. The protein sequence πi is aligned to the reference protein sequence π0, and a replication function ρ is calculated based on the score of the alignment and the deviation of the coding system size from the average coding system size in the population. See section Methods for details.