|Average execution times|
|ProGraphMSA noCS||191 s|
|ProGraphMSA CS||2351 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