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Possible bug #10
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Hey there and thanks for pointing this out! I poked around and I think that it's from a diff in the underlying energy functions and penalties applied to multibranching/bifurcations:
At the
In other words the energy functions and algo I adapted from those papers applies a greater penalty to bulge inbetween the branches than RNAFold: I'm not saying that I hope this helps for context. I'm thinking it might help folks if I write up a pinned issue summarizing the list of differences that I'm aware, of which this is one |
Also I appreciate this:
I hope the package remains useful |
Hi, I really like the package. A good alternative to Vienna (which isn't on pypi).
But when verifing your example sequence output against Vienna's RNAfold, it looks like seqfold misses two pair bonds? the lowercased g-c and a-u
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