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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.

From: SeqAn An efficient, generic C++ library for sequence analysis

 

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