Table 3.

Comparative orthology analysis on the Bac set

		SwiftOrtho		OrthoMCL	FastOrtho	OrthAgogue	OrthoFinder
Homology search	Method	SO built-in					N/A
	Hits	8,478,732,753					N/A
	Unique Hits	8,478,732,753					N/A
Orthology	(Co-)orthologs	876,766,940	N/A		950,683,849	N/A	N/A
inference	In-paralogs	622,292	N/A		663,052	N/A	N/A
Clustering	Algorithm	MCL	APC	MCL
	Orthologous groups	240,162	167,355	N/A	242,816	N/A	N/A

MCL: Markov clustering; APC: Affinity Propagation Cluster; N/A: not available.