Table 3. Benchmarks against simulated mammalian and fly genomic DNA.

Program	Blanchette et al.	DAWG	simgenome
	(Acc/Sn/PPV)	(Acc/Sn/PPV)	(Acc/Sn/PPV)
CHAOS/DIALIGN	0.58/0.44/0.74	0.72/0.46/0.43	0.62/0.67/0.59
DIALIGN-TX	0.73/0.68/0.77	0.72/0.51/0.44	0.64/0.68/0.61
FSA (–exonerate)	0.86/0.82/0.93	0.81/0.38/0.74	0.79/0.78/0.84
FSA (–exonerate –maxsn)	0.87/0.85/0.90	0.75/0.41/0.50	0.76/0.79/0.77
MAVID	0.57/0.45/0.68	0.66/0.36/0.32	0.72/0.77/0.72
MLAGAN	0.70/0.63/0.80	0.45/0.39/0.19	0.71/0.71/0.73
Pecan	0.92/0.91/0.92	0.77/0.48/0.53	0.78/0.81/0.78
TBA	0.83/0.81/0.87	0.80/0.32/0.75	0.74/0.79/0.72

Comparisons of the accuracies (Acc), sensitivities (Sn) and positive predictive values (PPV) of FSA and other alignment methods on simulated alignments of mammalian and Drosophila DNA. The simulated alignments of nonfunctional DNA sequences (“Blanchette et al.”) from nine mammals (human, chimp, baboon, mouse, rat, cat, dog, cow, and pig) were produced by [28]. Simulated alignments of nonfunctional (“DAWG ”) and functional as well as nonfunctional (“simgenome ”) DNA sequences from the twelve species of Drosophila described in [43] were produced with the DAWG [29] and simgenome [30] programs as described in [30] (both were parametrized based on Pecan alignments of Drosophila whole-genome alignments). Three of the simgenome alignments contained sequences of length zero and were removed from this analysis. FSA was run with the –exonerate option to use both anchors from the exonerate program as well as MUMs from MUMmer. FSA had the highest accuracy on the two simulated Drosophila datasets and only Pecan had higher accuracy on the mammalian dataset. Pecan consistently produced the most-sensitive aligments.