I'm trying to build a dependency parser and I want it to construct only projective trees.

Do you know any tool that converts Non-projective trees (CONLL-U format) to projective ones?

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I've just seen your question, I don't know whether it's still relevant, but here you have a paper that describes how to projectivise a dependency tree. http://www.aclweb.org/anthology/P05-1013

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