Table 3

Running time and memory use while performing diversity analyses

File

EggLib

libsequence

Time (s)

Memory (MB)

Time (s)

Memory (MB)


1000 files (49.8 MB) minimal

4.17

9.3

-

-

1000 files (49.8 MB) standard

9.54

9.5

12.34

1.8

1000 files (49.8 MB) LD

26.43

151.7

47.87

124.8

1 file (33.0 MB) minimal

4.35

104.0

-

-

1 file (33.0 MB) standard

6.84

92.6

2.63

44.1

1 file (6.0 KB) coding

0.16

8.7

0.06

0.1


Note: We analyzed 1000 simulated alignments of 50 sequences (plus one outgroup) of 1000 bp and a single alignment of 7 sequences of 4,920,321 bp. A subset of this alignment containing 6 sequences of 999 bp was analyzed for coding statistics. The minimal set of statistics was the number of polymorphic sites, θ estimators and Tajima's D. The standard set of statistics included minimal statistics plus haplotype-based statistics. Linkage disequilibrium (LD) was computed between polymorphic sites. For coding sequences, non-synonymous and synonymous θ estimators were calculated (for EggLib, the functions of Bio++ are called).

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

Open Data