Figure 8

Evolutionary dynamics of mean code scores in the course of minimization using the Gillis matrix as the measure of amino acid substitution cost. (a) The black circles show the mean score of the evolving random codes in the course of minimization vs arbitrary time units (pairwise swaps). Crosses show the mean values ± one standard deviation. The green line shows the cost of the standard code, and the blue shows the cost of the code that was obtained by minimization of the standard one. The top x-axis is the number of codes that did not reach their local minimum at the preceding step (starting from 300 random codes). The evolution of each code was followed until the code could not be improved anymore. (b) the number of codes that need exactly k pairwise swaps to reach minimum vs k; the blue line is the number of steps for the standard code to reach its local fitness peak (9); the red line is the mean of the distribution (19); (c) Same as (a) but the search started with 100 random codes that outperform the standard code; (d) Same as (b) but the search started with 100 random codes that outperform the standard code.