Table 1

Runtimes and internal space requirements for computing sequence alignments. The table shows average time and space requirements for aligning the genomes of two human influenca viruses, each of length about 15.6 kbp. Runtimes printed in bold face show for each library the time of the fastest algorithm for computing an alignment using edit distance.

linear gap costs

affine gap costs

time (s)

space (MB)

time (s)

space (MB)


SeqAn

Needleman-Wunsch

3.3

236

6.3

236

Hirschberg

14.7

4

Myers-Hirschberg

0.2

3

NCBI C++ toolkit

Needleman-Wunsch

4.0

245

Hirschberg

6.6

14

Bio++

13.4

2100

28.0

≈6000

BTL

96162

933

BioJava

76

2000

93

≈6000


Döring et al. BMC Bioinformatics 2008 9:11   doi:10.1186/1471-2105-9-11

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