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.

We have written a several papers about pplacer. The BMC Bioinformatics paper describes the v1.0 version of pplacer. There is also the following related work:

v1.1 binaries latest release
documentation manual tutorial
code github repository compilation
reference package software


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