Table 4.

F-score for pairwise comparison of alignment results for the M. tuberculosis dataset

	seq-seq-pan	Mugsy*	progressiveMauve	TBA	progressiveCactus
seq-seq-pan	-	0.996	0.991	0.975	0.934
Mugsy*	0.996	-	0.990	0.974	0.934
progressiveMauve	0.991	0.990	-	0.972	0.928
TBA	0.975	0.974	0.972	-	0.914
progressiveCactus	0.934	0.934	0.928	0.914	-

We estimate the similarity of alignments of progressiveMauve, Mugsy, progressiveCactus, seq-seq-pan and TBA, by calculating the pairwise F-score. The aligner with the most similar alignment is shown in bold for each aligner. * Aligning 43 M. tuberculosis genomes caused a segmentation fault in Mugsy. We were able to align 39 genomes and therefore compare the results only for this set of sequences