Timing comparison of FSA in regular and parallelized modes.

Runtimes for FSA in regular, �Cfast and �Cparallelize modes when aligning the 16S sequences of Table 11 sequences in unanchored mode (�Cnoanchored) with a 3-state HMM (�Cnoindel2) and refinement disabled (�Crefinement 0). When running in �Cfast mode on a cluster with 10 processors (3.00 and 3.20 GHz; 8 GB of RAM), FSA can align 500 16S sequences in 20% of the time required without parallelization. The parallelized FSA was run on a cluster managed by the Condor batch queueing system [66]; nodes were connected by a 100 Mbps Ethernet network. Note that these runtimes are much slower than users can expect from default FSA usage, which uses anchoring for speed (Table 11); we used unanchored mode to make clear the benefits of parallelization.