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. Here is the paper describing pplacer.
Pplacer was written by Frederick "Erick" Matsen, with very valuable input from Robin Kodner and Ginger Armbrust. Special thanks go to Chris Berthiaume and David Schruth at the Armbrust lab.
Here is a chart showing how long it takes to place 10,000 16s rRNA reads on reference trees of various size using pplacer; the reference alignment for these runs was 1287 nt long, and the query length was 198 nt. Tests run on an Intel Xeon @ 2.33 Ghz.
