Table 1 Version number and command-line arguments for each method

ClustalW 2.0 (iterative)

-Iteration = tree

ProbConsRNA 1.1

(default)

MAFFT-G-INS-i 6.516

mafft-ginsi

LaRA 1.3/1.31 *

(The default parameter file was used.)

Murlet 0.1

(default)

MXSCARNA 2

(default)

RNA Sampler 1.3

RNASampler_driver.pl -i 15 -S 100 > output

RNA Sampler 1.3 (fast)

RNASampler_driver.pl -i 15 -S 100 -f 1 > output

MASTR 1.0

(default)

X-INS-i-scarnapair 6.516

mafft-xinsi --scarnapair

X-INS-i-larapair 6.516

mafft-xinsi --larapair