David Coil edited Building a 16S rDNA Phylogenetic Tree.md  about 9 years ago

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5. Assign it a group name (this is what the program will label your sequence/organism). Choose this carefully since that will be the name on the final tree.   6. Click the "+" next to the sequence, to add it to your cart  7. Click on CLASSIFIER at the top of the page  8. Click on "Do Classification With Selected Sequences" button. This will show you a hierarchical view of the classification of your sequence (from Phylum to Genus.) You will use this information to navigate to other sequences that you want to include in your alignment that you will use to build your phylogenetic tree.For example, Figure \ref{fig:RDP} shows the hierarchy for the _Tatumella_ 16S sequence.  8. Click on BROWSERS. We recommend opening 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" (Figure 10).  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. Even better would be to chose an outgroup within the same bacterial phyla that you know to be outside of the clade you are examining. If in doubt, just use the Archaeal one.