As another example, line 301-4 states that "Simulating mutations ... is efficient" and refers to Fig 3 for evidence. The rest of the section (304-319) details a number of examples shown in Fig 3 that do not add much to the story.
We originally avoided contrasting the performance of sim_mutations with Pyvolve and SeqGen because it's hard to disentangle the method performance from inefficient file formats. The concrete examples were intended to sidestep this by showing that sim_ancestry is as fast as you'd ever need it to be, but this point was lost I think. So, better to use the space to run comparable mutation simulations in Pyvolve and SeqGen and report how long they took.
Reviewer 2 says:
We originally avoided contrasting the performance of sim_mutations with Pyvolve and SeqGen because it's hard to disentangle the method performance from inefficient file formats. The concrete examples were intended to sidestep this by showing that sim_ancestry is as fast as you'd ever need it to be, but this point was lost I think. So, better to use the space to run comparable mutation simulations in Pyvolve and SeqGen and report how long they took.