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Table 3 Average execution times

From: Fast and robust multiple sequence alignment with phylogeny-aware gap placement

Execution time

Mafft

27 s

Muscle

34 s

Muscle-i

157 s

ProGraphMSA noCS

191 s

Mafft-i

410 s

ClustalW

435 s

POA

448 s

ProGraphMSA CS

2351 s

Prank

12965 s

  1. Average execution times of the tested MSA tools estimated on the BAliBASE 3.0 benchmark. With a small number of sequences, as in this case, ProGraphMSA spends most of its execution time in the generation of context-specific profiles. With an increasing number of taxa we expect distance and tree estimation to consume an increasing share due to its quadratic time complexity.
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BMC Bioinformatics

ISSN: 1471-2105

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