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##Clean up the RDP taxon names  The RDP alignment will have taxon names that most of the downstream software tools will not tolerate because they consist of special text characters. So, we have written a little Perl script (cleanup.pl) that will remove those special characters and replace them with underscores. This script is included in the zip file of scripts on Figshare \cite{852a8297-50f7-4630-ae05-7645b7fb6d11}. \cite{47b41cbb-81bb-44cb-8430-1218ddad365c}.  To run cleanup.pl, first move it to your Applications folder. Then, in a Terminal window, navigate to the directory that contains the RDP alignment that you've just downloaded. Then, type or copy/paste: perl /Applications/cleanup.pl -i RDP_alignment.fa -o RDP_alignment_clean.fa