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Table 1 Command line options for the programs in the experiments. This table summarizes multiple alignment programs and their command line options used in the paper.

From: A fast structural multiple alignment method for long RNA sequences

Program Command
MXSCARNA ./mxscarna <input_filename>
Murlet ./murlet -max_time = 100 <input_filename>
ProbCons ./probcons <input_filename>
MAFFT ./mafft <input_filename>
ClustalW ./clustalw <input_filename>
StrAl ./stral <input_filename>
RNASampler perl RNASampler_driver.pl -p <input_dir> -q <input_filename> -i 15 -S 100
RNAlara ./lara -i <input_filename>
Locarna ./mlocarna -struct-local = false -sequ-local = false <input_filename>
FoldalignM-Foldalign perl FoldalignM_Foldalign.pl -f <input_filename>
FoldalignM-McCaskill java FoldalignM_McCaskill <input_filename>
MARNA perl marna.pl -g 2 <input_filename>
PMmulti perl pmmulti.pl <input_filename>
stemloc ./stemloc -g -m -slow <input_filename>