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资源说明：Phylogenetic placement and downstream analysis
# pplacer suite of programs [](https://app.wercker.com/project/bykey/b3fe580ff3a62d0a69c6da264c03ba81) `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. * [project webpage (with compiled binaries)](http://matsen.fhcrc.org/pplacer/) * [documentation](http://matsen.github.io/pplacer/) * [tutorial](http://fhcrc.github.io/microbiome-demo/) * [compilation instructions](http://matsen.github.io/pplacer/compiling.html) `pplacer`, `guppy`, and `rppr` are free software under the GPL v3. ### Related tools Several other tools have used pplacer as one of their main components. Some of these include: * **SEPP** ([Mirarab, Nguyen, Warnow, PSB, 2012](http://www.worldscientific.com/doi/abs/10.1142/9789814366496_0024)) 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](github.com/smirarab/sepp) can place on the GreenGenes dataset with 200,000 sequences. A standalone version for the GreenGenes reference is available [here](https://github.com/smirarab/sepp/wiki/SEPP-on-Greengenes). * **paprica** ([Bowman and Ducklow, PLOS One, 2015](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0135868)) 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](https://github.com/bowmanjeffs/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](http://www.polarmicrobes.org/analysis-with-paprica/).
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