Table 4.

Average wall-clock running time (hr) across most full-length datasets

Method	ROSE	RNASim	Indelible	ROSE	CRW	10 AA	HomFam	HomFam
	NT	10K	10K	AA			(17)	(2)
UPP	0.6	6.7	6.7	0.2	11.6	<0.1	1.3	0.5
PASTA	0.6	3.9	1.3	0.2	3.2	0.2	1.5	1.3
MAFFT	0.4	0.1	1.4	<0.1	0.4	0.1	<0.1	0.1
Muscle	0.5	0.8	1.2	<0.1	5.9	0.2	1.3	X
Clustal	0.4	4.8	X	0.1	2.8	<0.1	0.3	0.3

Average wall-clock running time for the full-length datasets for which most methods could complete; this includes everything other than the RNASim datasets with 50,000 or more sequences. UPP is run in default mode. Results marked with an X indicate that the method failed to terminate within the time limit (24 hours on a 12-core machine). All methods but Muscle had parallel implementations and were able to take advantage of the 12 cores. Muscle failed to align two of the HomFam datasets; we report separate average results for the 17 HomFam datasets for all methods and the two HomFam datasets for all but Muscle.