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> |