Table 7.

Performance of ProbCons Variants on SABmark “Twilight Zone” set

Algorithm	c	Ir	Output	fD	fM	Time (mm:ss)
1. Viterbi	0	0	Pairwise	27.5	17.2	0:42
2. Posterior	0	0	Pairwise	29.6	18.5	2:54
3. Posterior	1	0	Pairwise	32.5	20.4	3:15
4. Posterior	2	0	Pairwise	33.2	21.0	3:47
5. Posterior	0	0	Multiple	29.1	19.8	2:57
6. Posterior	1	0	Multiple	30.9	20.8	3:17
7. Posterior	2	0	Multiple	31.5	21.3	3:50
8. Posterior	0	100	Multiple	30.6	20.8	4:14
9. Posterior	2	100	Multiple	32.1	21.7	5:50

The first column indicates whether the Viterbi algorithm (highest probability alignment) or posterior decoding (maximal expected accuracy alignment) was used. The next two columns indicate c, the number of iterations of the consistency transformation used, and ir, the number of rounds of iterative refinement used as post-processing. The fourth column indicates whether the ProbCons was set to generate all-pairs pairwise alignments or consistent multiple alignments. The next two columns show the average developer (f_D) score (equivalent to sum-of-pairs [SP] score) and modeler (f_M) score achieved by each aligner for the “Twilight Zone” set in the SABmark database. The last column gives the total running time for each method over all 236 alignments. All scores have been multiplied by 100. Note that the last row corresponds to the parameter settings that are the default in the ProbCons program. The best results in each column are shown in bold.