Table 2.

Average alignment SP-error, tree error, and TC score across most full-length datasets

Method	ROSE	RNASim	Indelible	ROSE	CRW	10 AA	HomFam	HomFam
	NT	10K	10K	AA			(17)	(2)
Average alignment SP-error
UPP	7.8 (1)	9.5 (1)	1.7 (2)	2.9 (1)	12.5 (1)	24.2 (1)	23.3 (1)	20.8 (2)
PASTA	7.8 (1)	15.0 (2)	0.4 (1)	3.1 (1)	12.8 (1)	24.0 (1)	22.5 (1)	17.3 (1)
MAFFT	20.6 (2)	25.5 (3)	41.4 (3)	4.9 (2)	28.3 (2)	23.5 (1)	25.3 (2)	20.7 (2)
Muscle	20.6 (2)	64.7 (5)	62.4 (4)	5.5 (3)	30.7 (3)	30.2 (2)	48.1 (4)	X
Clustal	49.2 (3)	35.3 (4)	X	6.5 (4)	43.3 (4)	24.3 (1)	27.7 (3)	29.4 (3)
Average ΔFN error
UPP	1.3 (1)	0.8 (1)	0.3 (1)	1.8 (1)	7.8 (2)	3.4 (2)	NA	NA
PASTA	1.3 (1)	0.4 (1)	<0.1 (1)	1.3 (1)	5.1 (1)	3.3 (1)	NA	NA
MAFFT	5.8 (2)	3.5 (2)	24.8 (3)	4.5 (3)	10.1 (3)	2.3 (1)	NA	NA
Muscle	8.4 (3)	7.3 (3)	32.5 (4)	3.1 (2)	5.5 (1)	12.6 (3)	NA	NA
Clustal	24.3 (4)	10.4 (4)	X	4.2 (3)	34.1 (4)	3.5 (2)	NA	NA
Average TC score
UPP	37.8 (1)	0.5 (2)	11.0 (3)	2.6 (2)	1.4 (1)	11.4 (1)	47.3 (1)	40.3 (3)
PASTA	37.8 (1)	2.3 (1)	48.0 (1)	5.4 (1)	2.3 (1)	12.1 (1)	46.1 (2)	50.0 (1)
MAFFT	31.4 (2)	0.4 (2)	7.8 (4)	0.6 (3)	0.7 (2)	12.1 (1)	45.5 (2)	46.9 (2)
Muscle	9.8 (3)	<0.0 (2)	18.3 (2)	2.7 (2)	0.7 (2)	10.5 (2)	27.7 (4)	X
Clustal	5.7 (4)	0.2 (2)	X	3.1 (2)	0.1 (2)	11.8 (1)	38.6 (3)	31.0 (4)

We report the average alignment SP-error (the average of SPFN and SPFP errors) (top), average ΔFN error (middle), and average TC score (bottom), for the collection of full-length datasets. All scores represent percentages and so are out of 100. Results marked with an X indicate that the method failed to terminate within the time limit (24 hours on a 12-core machine). Muscle failed to align two of the HomFam datasets; we report separate average results on the 17 HomFam datasets for all methods and the two HomFam datasets for all but Muscle. We did not test tree error on the HomFam datasets (therefore, the ΔFN error is indicated by “NA”). The tier ranking for each method is shown parenthetically