cove, infernal, or text format input question

[byee4]

Hi, I'd like to try this tool out but am wondering how to format the infernal, cove, or text files properly. It appears that at one point there may have been an Appendix section in the readme, but I'm unsure how to reproduce the example or run tSFM. Could dot notation-style files be used or converted into an acceptable format?

c. The -c option provides the path to the file containing the secondary structure annotation in cove format for RNA input files. This is required for basepair function logos and can be provided in infernal, cove, or text formats. These formats are described in below in the Appendix section. The secondary structure annotation must conform to and encode the RNA structural alignment common to the input alignment files and usually must be prepared together with them.

[dhard]

Hello! Sorry for the long delay to answer your question. Here is a quick and incomplete answer, with an example of cove format:

=CS >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<.