IQ tree supposedly supports ambiguities in its input alignments. However, when I submit a job it keeps returning errors like this "ERROR: State specified (r) for taxon 39, character 665, not found in list of valid symbols". It doesn't matter if I am using CIPRES or the web server (http://iqtree.cibiv.univie.ac.at). Has anyone who used IQ tree before encountered the same problem? Is there a way around without editing every ambiguity?

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