Table 11. Timing comparison of FSA and other methods on 16S sequences.
Program | 100 | 200 | 300 | 400 | 500 seqs |
ClustalW | 1,194 s | 4,147 s | 9,110 s | 16,187 s | 27,755 s |
DIALIGN | 4,346 s | 19,449 s | 49,388 s | (fail) | (fail) |
FSA –fast | 1,513 s | 3754 s | 5,641 s | 9,767 s | 15,683 s |
FSA –fast –noindel2 –refinement 0 | 638 s | 1,495 s | 2,467 s | 3,604 s | 5,154 s |
MAFFT | 31 s | 105 s | 243 s | 442 s | 54 s |
MUSCLE | 351 s | 1,235 s | 1,516 s | 4,384 s | 7,552 s |
ProbConsRNA | 16,319 s | (fail) | (fail) | (fail) | (fail) |
T-Coffee | 1,362 s | 3,666 s | 7,880 s | 15,254 s | 22,085 s |
SeqAn::T-Coffee | 3,024 s | (fail) | (fail) | (fail) | (fail) |
Comparison of runtimes of FSA and other alignment methods when aligning 16S ribosomal sequences. MAFFT was faster than any other method by an order of magnitude; the next-fastest programs were MUSCLE and FSA. FSA can be made substantially faster by using a 3-state, rather than the default 5-state, HMM (with little loss of accuracy; see Table 8) and disabling iterative refinement. MAFFT was run with the –auto option, which presumably triggered a faster alignment mode on the 500 sequence dataset than was used for the datasets with fewer sequences. The designation “(fail)” means that a programs failed to align a dataset (generally due to out-of-memory errors). Timing results are from computers with 2.40 GHz CPUs and 2 GB of RAM. 16S sequences were obtained as a random slice of prokMSA from Greengenes [65] and had an average length of 1,450 nt.