Table 3.

Precision, Recall and F-Score for alignments of the simulated dataset

	Precision	Recall	F-score
TBA	0.993	0.999	0.997
progressiveMauve	0.992	0.477	0.644
seq-seq-pan	0.993	0.475	0.643
Mugsy	0.999	0.474	0.643
Mugsy with duplications	0.999	0.474	0.643
progressiveCactus	0.892	0.473	0.618
progressiveCactus with duplications	0.999	0.339	0.506

We compare the results of all alignment tools with the true alignment of the simulated genomes. Aligners are sorted first by F-score and then by Recall