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Table 5 Running time and memory use while performing ABC

From: EggLib: processing, analysis and simulation tools for population genetics and genomics

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
  1. 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: 0-0.05 (per site) for the mutation and recombination rates, 0.01-1 for the migration rate, 0-1 for date/duration parameters, 0-1 for the population size during bottleneck 0-10 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 bp-long 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.