Timing comparison of FSA and other methods on 16S sequences.

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.