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: 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.

De Mita and Siol BMC Genetics 2012 13:27   doi:10.1186/1471-2156-13-27

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