Pplacer

Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.

Pplacer was developed by the Matsen Group at Fred Hutch. More information can found here:
http://matsen.fhcrc.org/pplacer/

Here are some info to install all the dependencies to run pplacer:
Installation

Here is a quick tutorial to run pplacer:
Pipeline