Table 2.

AYbRAH ortholog database statistics before and after curation. The initial ortholog assignments were obtained with OrthoMCL and OrthoDB. Additional proteins were annotated using TBLASTN. Ortholog groups for enzymes and small metabolite transporters were manually curated by visual inspection of homolog phylogeny and by identifying ortholog groups with an ETE 3 script (40). Ortholog groups were modified by adding unannotated proteins to existing groups via pplacer (41) or by collapsing multiple ortholog groups into a single ortholog group if there were no gene duplications in the homolog group (under-clustering)

	AYbRAH
	v0.1	v0.2.3
Proteins	212 551	214 498
Proteins in AYbRAH	169 118 (79%)	187 555 (87%)
Fungal ortholog groups	14 249	22 538
Homolog groups	0	18 202
Manually curated ortholog groups	0	625
Electronically modified ortholog groups	0	3760