The genotype encodes the phenotype of a digital organism.

The genotype of a digital organism with the smallest genome required to perform the logic operation NAND is depicted as a circular set of 12 instructions (represented here as letters). Beyond the instructions necessary for copying the genome, the genetic language of Avida contains instructions for storing and manipulating 32-bit binary numbers in buffers (input-1 and input-2) and registers (AX, BX, and CX). Each binary number is represented here as a sequence of 32 boxes, one for each bit. The value of each bit is depicted as a black box if it equals one and as a white box if it equals zero. The cartoon shows the execution of the input-output instruction (represented by the letter y; highlighted in black). (A) The state of the input buffers and registers before executing the input-output instruction (the arrow points toward the next instruction to be executed). (B) The state of the input-buffers, registers, and the output after executing the input-output instruction. The input-output instruction outputs the number stored in the BX register, checking for any logic operation that may have been performed on the two binary numbers previously stored in the input buffers. In this example, the output is the result of applying the logic operation NAND: for each bit pair, the result is 0 (white box) if and only if the two bits are 1, and 1 otherwise (red box). Then, the input-output instruction places a new random binary number into the BX register (a number that is also stored in the input-1 buffer after moving the number previously stored there to the input-2 buffer). The complete step-by-step self-replication cycle of this digital organism is shown as S1 Appendix. Note that, in our study, the genome of digital organisms is much larger (i.e., 100 instructions long).