deletions | additions       diff --git a/Building a 16S rDNA Phylogenetic Tree.md b/Building a 16S rDNA Phylogenetic Tree.md  index 6827574..8391cb8 100644  --- a/Building a 16S rDNA Phylogenetic Tree.md  +++ b/Building a 16S rDNA Phylogenetic Tree.md 
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perl /Applications/CleanupRDP.pl -i RDP_alignment.fa -o RDP_alignemnt_clean.fa  ##Building the Tree with FastTree   There are two ways to get FastTree, which will be required for building the tree from your alignment. The first is to jump ahead to section 10.1.4 and install Phylosift which contains a working version of FastTree. In this case, you will simply call the program from the Phylosift directory with the following command (be sure the path to Phylosift is correct):  /phylosift/osx/FastTree -nt RDP_alignemnt_clean.fa > tree_file.tre  The other option is to install FastTree directly, which is a bit more involved.  Go to http://www.microbesonline.org/fasttree/#Install  and download the FastTree.c program by right clicking on it and saving the link to your Applications folder. To compile the software, navigate to your Applications folder in a Terminal window: