Both the MUTAGENIZE and CROSS functions ask that you specify how many phages are used in the experiment. That's quite reasonable -- the more phages you mutagenize, the more mutants you'll get, and the more phages you cross, the more progeny you get. The simulation needs to know this number. And so do you. If you choose a number too small, you'll get zero plaques -- useless. If you choose a number too large, you'll get so many plaques that they run together -- equally useless. In this simulation, you can cram no more than 1500 plaques on a plate before they run together. But there's much else you need to know in order to figure out how many phages to use in an experiment. If you're doing a mutagenesis experiment, you need to know that [10]: The mutagenesis process kills off ~75% of the phage Of those that survive, about 0.5% are R- mutants Of the R- mutants, most are from mutations in either rIIA or rIIB (mostly rIIA) For the purposes of this simulation, spontaneous mutation to R- doesn't happen If you're doing a cross, you need to know that [11,12]: The rate of recombination is proportional to the distance between the sites of interest The rate of recombination between a site at the beginning of rIIA and a site at the end of rIIA is about 5% rIIB is about half the size of rIIA For the purposes of this simulation, the recombination rate has been deemed to be ten-times the natural rate! This is so to decrease the number of plaques you need to screen to get the desired constructs. I wanted to keep the simulation as close as possible to reality, but reality took many many months so forgive me this change.