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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