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

From: Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

Method Arguments
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
  1. * As the latest version of LaRA (1.31) frequently aborted for cases with more than two sequences, version 1.3 was used together with the parameter file of version 1.31.