Table 1. Comparison of tools for automated CAZyme annotation.

	Accuracy (F-score)
Tools + databases	Bacteria	Eukaryotes	Subfamily	Multi-family proteins	Domain repeats	Domain positions	Speedc
HMMER+dbCAN	0.88	0.86	Yesa	Yes	Yes	Yes	69
DIAMOND+CAZy	0.89	0.84	Yesa	No	No	No	4
Hotpep+PPR	0.80	0.94	Yesb	Yes	No	No	7
Predicted by > = 2 tools	0.93	0.92

^aTwenty four CAZyme families are classified into 207 subfamilies by phylogenetic clustering and CAZy expert curation (10).

^bThree hundred and forty two CAZyme families are classified into 7036 groups by PPR (15,16).

^cThe time is in seconds and calculated on Escherichia coli K-12 MG1655 proteome (4140 proteins). The detailed calculations on accuracy and speed are available in Supplementary Table S1. No correspondence has been established between PPR groups and CAZy subfamilies, and in dbCAN web server we only report CAZy subfamily annotation, whenever it is available.