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

Open Data