deletions | additions       diff --git a/Building a 16S rDNA Phylogenetic Tree.md b/Building a 16S rDNA Phylogenetic Tree.md  index 3f1d394..075a18e 100644  --- a/Building a 16S rDNA Phylogenetic Tree.md  +++ b/Building a 16S rDNA Phylogenetic Tree.md 
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8. Click on BROWSERS. We recommend openining BROWSERS in a new tab so that you can keep the hierarchy information handy.  9. Click on "Isolates" to select only isolates for further analysis. Then click "Browse"  10. Click on the + sign next to "Archaea outgroup." This will add an Archaeal sequence to your cart, which will be used to root your phylogenetic tree.  11. If using the example sequence provided, click on "Proteobacteria", then Gammaproteobacteria, then "Enterobacteriales", then Enterobacteriaceae. This will take you to the Genus Tatumella, which currently has over 69 species in it. If the genus you are working with has too many sequences to analyze easily (for example, _Bacillus_ currently has >26000,) one way to reduce this number is to exclude the uncultured taxa in the database. To do this, scroll down to the Data Set Options and click on the "Isolates" button. Click "Refresh" and you will see that there are fewer sequences in the Genus. To reduce this number further, click on the "Type" Strain button. button (though if you do this you'll have to build a tree later for species identification since each species will only be represented once in the tree).  As a worst-case scenario, you will need to manually select a subset of organisms to include in your alignment. 12. Click on the + sign next to **genus** Tatumella to add all of those sequences to your cart.  13. Click on "Sequence Cart" and confirm that your uploaded sequence, the outgroup sequence, and all of the other sequences you'd like to include in your tree are displayed.  14. Click on "download," leave the download options as the defaults (fasta, aligned, uncorrected ,) uncorrected,)  and then click on the appropriate download button. Save the file and then rename it to something informative. ##Clean up the RDP taxon names 
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  In tree shown above (genus Brachybacterium), our sample of interest from an assembly is "Brachybacterium muris UCD-AY4" \cite{Lo\_2013}. 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 monophyletic clade of _Brachybacterium muris_.    UPDATE THIS FOR TATUMELLAIn In  the tree shown above (genus Tatumella) our species of interest is Tatumella sp. \cite{Bendiks_2013}. 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.