Table 5 

Running time and memory use while performing ABC 

Simulation step 
Egglib 
msABC 

Model + summary statistics 
Time (s) 
Memory (MB) 
Time (s) 
Memory (MB) 


SNM + SDZ 
13.71 
25.6 
7.24 
8.9 
SNMR + SDZ 
27.09 
55.6 
26.10 
8.8 
PEMR + SDZ 
16.72 
44.8 
13.46 
8.6 
BNM + SDZ 
15.68 
37.6 
8.27 
9.1 
IM + SDZ 
40.06 
70.3 
21.52 
14.2 
AM + SDZ 
25.11 
57.8 
* 
* 
SNM + SFS 
15.83 
25.8 
 
 
SNMR + SFS 
29.85 
55.6 
 
 
PEMR + SFS 
18.05 
44.9 
 
 
BNM + SFS 
18.22 
36.5 
 
 
IM + SFS 
46.94 
63.6 
 
 
AM + SFS 
29.15 
51.6 
 
 


Analysis step 
ABCreg 



Data file: 830 MB 
70.82 
131.0 
30.74 
628.7 


Note: Models: standard neutral model (SNM), standard neutral model with recombination (SNMR), population expansion model with recombination (PEMR), bottleneck model (BNM), island model with two populations (IM), admixture model (AM). Uniform prior bounds: 00.05 (per site) for the mutation and recombination rates, 0.011 for the migration rate, 01 for date/duration parameters, 01 for the population size during bottleneck 010 for the ancestral population size. Summary statistics sets: SDZ (number of polymorphic sites, Tajima's D and Fay and Wu's H), SFS (site frequency spectrum with 8 categories). The SFS was available only with EggLib. 20 loci of 40 sequences 1000 bplong were analyzed and each ABC simulation run generated 1000 data samples. For the analysis phase, a large data set of 5,000,000 samples (containing two varying model parameters and nine statistics) was used. EggLib was used through the interactive commands abc_sample and abc_fit. (*) The AM model could not be implemented with msABC. 

De Mita and Siol BMC Genetics 2012 13:27 doi:10.1186/147121561327 