deletions | additions       diff --git a/Building a 16S rDNA Phylogenetic Tree.md b/Building a 16S rDNA Phylogenetic Tree.md  index 21b1c40..fe4cf05 100644  --- a/Building a 16S rDNA Phylogenetic Tree.md  +++ b/Building a 16S rDNA Phylogenetic Tree.md 
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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 find navigate to  other sequences that you want to include in your alignment that you will use to build your phylogenetic tree. For example, Figure X shows the Hierarchy for _Bacillus subtilus_.  8. Under "Data Click on BROWSERS. We recommend openining BROWSERS in a new tab so that you can keep the hierarchy information handy.  9. 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.  10. If using the example sequence provided, click on Firmicutes, then Bacilli, then Bacillales, then Bacilaceae. This will take you to the Genus Bacillus, which currently has over 26,000 species in it. 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," Options and click on the "Isolates" button. Click "Refresh" and you will see that there are still more than 22,000 sequences in the Genus. To reduce this number further, click on the "Type" Strain button. This will result in a reasonable number of 181 taxa.  11. Click on the + sign next to **genus** Bacillus to add all of those sequences to your cart.  12. Click on TREE BUILDER  13.  Specify isolates as your outgroup. At  the Source, leave time of publication,  the rest as defaults Archaeal outgroup is Methanocaldococcus.  14. Click "Create Tree"    Note: RDP will not generate trees with more than 200 sequences. However, if following our recommendation of using Fasttree then this limit does not apply. You can check how many sequences are in your cart by looking to the right of "Hierarchy Browser".  Click Browse   Browse Sequences  To choose a specific bacteria click on the blue class/subclass/order button until you see a specific species and click the plus next to it. If you want to choose an entire class/subclass/order, click on the plus sign next to it. Note: RDP will not generate trees with more than 200 sequences. However, if following our recommendation of using Fasttree then this limit does not apply. You can check how many sequences are in your cart by looking to the right of "Hierarchy Browser". In most cases the tree should can  be built with sequences from other isolates within the same genus. For a genus with relatively few sequences in RDP, this is fairly straightforward; select the entire genus and move on to choosing an outgroup. For genera with very large numbers of sequences, trimming is required. Since the goal is to discover the placement of a candidate sequence within the genus, the best pool of sequences would contain multiple sequences from each species in that genus. This requires manual selection of sequences in the Browser. We recommend avoiding using  sequences without with  informative names.Select an outgroup   The ideal outgroup is a sequence as closely related to your candidate as possible, but outside the group that you want to examine. We recommend choosing a type sequence from within the same family.  Click on TREE BUILDER  Specify your outgroup (make a note of your outgroup because you will need it when viewing the alignment in Dendroscope  Click on Create tree  In some rare cases the tree generated by RDP will be sufficient, other times it may fail to load, crash, or be impossible to resolve detail. We recommend instead, downloading the alignment and building the tree in FastTree.