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Table 1 Performance gains with ancestry-based simulation

From: Rapid forward-in-time simulation at the chromosome and genome level

 

N e = 1,000; L= 5·106

N e = 5,000; L= 106

AF, F=100%

20.2 secs

128.9 secs

AF, F=10%

3.0 secs

32.6 secs

AF, F=1%

2.0 secs

26.6 secs

AF, F=0%

1.3 secs

16.5 secs

SFS_CODE

427.3 secs

2910.4 secs

  1. AnA-FiTS (AF) runtimes (in sec) for simulation of neutral sequences with a varying proportion F of mutations simulated forward in time (e.g., F:=10%⇒ 10% of mutations are simulated forward in time, 90% using the BEG algorithm); SFS_CODE runtime for comparison. Simulations for 10·N e generations, with per-base recombination and mutation frequency of 2.5·10−8.