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Hi, getting parts of the tree has never been supported with NexSON. I have just clarified that in the README. I agree that the "cannot convert..." error messages are not helpful and should be more targeted.
This is the result of the call used in the documentation:
By pulling a Homer, I fluked upon a permutation that worked by specifying a newick return:
This also works with Nexus. So the problem seems to be localized to nexson.
@jimallman suggested appending
&output_nexml2json=1.2.1
:but that did not work.
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