pplacer suite of programs
pplacer places reads on a phylogenetic tree.
guppy (Grand Unified Phylogenetic Placement Yanalyzer) yanalyzes them.
rppr is a helpful tool for working with reference packages.
rppr are free software under the GPL v3.
Several other tools have used pplacer as one of their main components. Some of these include:
SEPP (Mirarab, Nguyen, Warnow, PSB, 2012) aims to improve the scalability of phylogenetic placement using divide-and-conquer. It uses Ensembles of Hidden Markov Models (implemented by HMMER) to both align sequnces and to find a (small) subtree for placement using pplacer. SEPP can place on the GreenGenes dataset with 200,000 sequences. A standalone version for the GreenGenes reference is available here.
paprica (Bowman and Ducklow, PLOS One, 2015) uses Infernal and pplacer to place reads on a reference tree of 16S rRNA genes from all completed genomes in Genbank. The domains Bacteria, Archaea, and Eukarya are all supported. paprica normalizes for 16S rRNA gene copy number and provides and estimate of the enzymes, metabolic contents, and genomic character (e.g. GC content, genome length) of the community. It is available as an Amazon Machine Instance or VirtualBox appliance, however, we recommend that you install the dependencies and run locally. A basic tutorial can be found here.