Table 3

Average execution times
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

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.

Szalkowski

Szalkowski BMC Bioinformatics 2012 13:129   doi:10.1186/1471-2105-13-129

Open Data