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#Building a 16S rDNA Tree  What _is_ this thing? At this point, you have an organism in pure culture, but you do not know what it is. If you found a creature crawling on the ground and  wanted to identify (or classify) it, you might look at it's morphology and ask what it most _looks_ like. If it has six legs, you might hypothesize it is some kind of  insect. If it has hard outer wings folded over its back, you might hypothesize that it is some kind of beetle. If it also had antler-style horns on its head, you might  hypothesize that it is some kind of stag beetle. If you do not have enough information available to hypothesize what kind of stag beetle you have, then you have reached the  limit of *taxonomic resolution* for your creature.   With an unknown microbial species, the best way to identify it is to sequence one of its genes (most people  use the 16S rRNA gene) and ask what _it_ most looks like. With animal classification, commonly used key features are things like legs and wings and horns; with microbial  classification, the key features to examine are the nucleotides in different positions in a DNA sequence. Fortunately, we have computer programs to help us make  sense of the DNA sequence information. Our preferred approach to classifying microbial species is to place an the  unknown sequence organism  in the context of a phylogenetic tree of known sequences. using its 16S rRNA gene sequence.  Building a phylogenetic tree from a 16S rRNA sequence is fairly straightforward, but the interpretation of the tree can be a bit complex. Here, we attempt to guide you through both. However, some complicated cases will require consultation with an expert in the field of phylogenetics or systematics. The outline of the workflow is to use the Ribosomal Database Project (RDP) to generate an alignment of the sequence with close relatives and an outgroup,  following outgroup. This is followed  by cleanup of the RDP headers, tree-building with FastTree FastTree,  and viewing/interpretation of the tree using Dendroscope. ##Obtain an RDP alignment