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Brackets "(" and ")" should be removed from partition names when uploading an alignment to beauti. If the file name contains a bracket (which it shouldn't, but sometimes does), the partition will have a bracket by default, and then there will be brackets in the newick file (e.g., on branch rates) and the newick file will not parse using the beast machinery.
Same logic applies for other symbols that have a meaning in annotated newicks although I have not tested those ones -- ;&[]{}