Suboptimal tracebacks collapsing CTDs

[maxhwardg]

In RNA design problems, a designer usually specifies only the base pairs and not the CTDs. It would be convenient to have a method to get suboptimal tracebacks but collapse structures that are the same modulo CTDs somehow. I am not sure what the best way to do this is. It is conceptually similar to a how a base pair probability table collapses information on a per base pair level.

[Edgeworth]

There is a way to get CTD-less suboptimal tracebacks IIRC, I've done it before. I'll update when I remember the details.

[maxhwardg]

In general, I think it would be beneficial to have options to turn on/off CTDs in all the algorithms. Also, an option to simulate the heuristic Vienna does.

[Edgeworth]

Agree w.r.t. CTDs, it's on my list already actually. For Vienna maybe we can run it through bridge.

[Edgeworth]

We have none/D2/no-coax support now, which is probably enough for this?