deletions | additions       diff --git a/Building a 16S rDNA Phylogenetic Tree.md b/Building a 16S rDNA Phylogenetic Tree.md  index 37d4b29..131e5a6 100644  --- a/Building a 16S rDNA Phylogenetic Tree.md  +++ b/Building a 16S rDNA Phylogenetic Tree.md 
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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 (CleanupRDP.pl) that will remove those special characters and replace them with underscores. This script will be is  included in the data download from github. zip file of scripts on figshare(http://figshare.com/articles/Miscellaneous_Scripts_for_Workflow/1086285).  To run CleanupRDP.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: perl /Applications/CleanupRDP.pl -i RDP_alignment.fa -o RDP_alignemnt_clean.fa