deletions | additions       diff --git a/Building a 16S rDNA Phylogenetic Tree.md b/Building a 16S rDNA Phylogenetic Tree.md  index 643d526..ad88a86 100644  --- a/Building a 16S rDNA Phylogenetic Tree.md  +++ b/Building a 16S rDNA Phylogenetic Tree.md 
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$ perl /Users/microBEnet/Desktop/RDPcleanup.pl -i /Users/microBEnet/Desktop/newTatumella.fa -o TatumellaRAST_RDP.fa  ##Building the Tree with FastTree   Go to http://www.microbesonline.org/fasttree/#Install and download the FastTree.c program by right clicking on it and saving the link link. Move the FastTree.c file to your Applications folder. To compile the software, navigate to your Applications folder in a Terminal window  FastTree requires a gcc compiler to function? Which you can download and install from xcode here  https://developer.apple.com/downloads/index.action?q=xcode cd /Applications  Then, type:  In order to download xcode you will need to register as a developer with Apple which takes only a couple minutes. gcc -O3 -finline-functions -funroll-loops -Wall -o FastTree FastTree.c -lm  After downloading xcode follow FastTree requires a gcc compiler. If  your computer’s instructions attempt  to install it. Once it compile FastTree fails, this  isinstalled open the program and open preferences (under the xcode tab). Click on  the downloads option most likely reason. You can download  and install the command line tools. gcc compiler from Xcode here https://developer.apple.com/downloads/index.action?q=xcode  Once In order to download Xcode  you have successfully downloaded will need to register as a developer with Apple which takes only a couple minutes. After downloading Xcode follow your computer’s prompts to install it. Once it is installed, open the program  andinstalled xcode,  open preferences (under the Xcode tab). Click on  theterminal, navigate to your  downloads file (or wherever you are storing FastTree) and copy option  and paste install  the following syntax command line tools.  $ gcc -O3 -finline-functions -funroll-loops -Wall -o FastTree FastTree.c -lm Once you have successfully downloaded and installed Xcode, return to your Applications folder in your Terminal window and type:  To run FastTree, type the following in the terminal  $  FastTree -gtr -nt alignment.file your_alignment_file  > tree_file tree_file.tre  For Example  $ /Users/Madison/Downloads/FastTree -gtr -nt /Users/Madison/Desktop/newTatumella > /Users/Madison/Desktop/tree_file_tatumella.tre The alignment file will be the output file of the cleanup script script.  And the tree_file output name should include a path to where you want it to be located. The output name should also end ends  in .trein order  to ensure that it will  be recognized by Dendroscope Dendroscope.  ##Viewing the Tree in Dendroscope  Download and install Dendroscope 
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You will need to obtain a license here  http://www-ab2.informatik.uni-tuebingen.de/software/dendroscope/register/  Enter the license into Dendrosope and then you can open your alignment from the File menu  to view it (file it.  Once the tree is visible, the first step is to re-root the tree to the outgroup. Expand the tree by clicking the expansion button (labeled in the above screen shot), Figure X),  then scroll through the tree to locate the outgroup. Click on the beginning of the taxa name, to select it, and reroot the tree by going to edit and selecting re-root. We recommend viewing the tree as a phylogram which can be accomplished by clicking on the phylogram button (labeled in the above screen shot). Figure X).  From this tree it should be possible to determine the phylogenetic placement of the candidate sequence, and in some cases to give it a name with more certainty than a simple BLAST search. Below are examples of a relatively informative tree and a relatively uninformative tree: TI    In tree shown above (genus Brachybacterium), our sample of interest from an assembly is "Brachybacterium muris UCD-AY4" (REF). It falls within a clade where every named member has the same name "Brachybacterium muris", and this name does not occur elsewhere on the tree. Hence, we were confident enough to name our sample as that species. In other words, this sequence falls within a well-supported (note 0.999 bootstrap support,) monophyletic clade of _Brachybacterium muris_.    In the tree shown above (genus Microbacterium) our species of interest is Microbacterium sp. str. UCD-TDU (REF). In contrast to the Brachybacterium example, here our species falls within a poorly defined clade containing multiple species. In this case we did not assign a species name to this isolate.