| RNAstrand [options] -i [input alignment] -r [reverse complementary alignment] |
| -i | Input alignment in either CLUSTALW (default) or MAF (-a option) format. |
| -r | Reverse complementary alignment. Use utils/rcAln.pl to get a CLUSTALW-realigned reverse complement. rcAln.pl assumes that clustalw is installed on your system. |
| -f from -t to | Scans only subregion of the input alignment. |
| -s c | Threshold value c of RNAstrand score, default: c=0.0001. |
| -a | Alignment in MAF format. If -a is missing: alignment in CLUSTALW format. |
| -h | Output help information. |
| -v | Output version information. |
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Updated:
29 May 2007