Handling and analysis of high-throughput phylogenetic sequence data.

Bioconductor version: Release (2.11)

phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of phylogenetic sequencing data.

Author: Paul J. McMurdie <mcmurdie at>, Susan Holmes <susan at>

Maintainer: Paul J. McMurdie <mcmurdie at>

To install this package, start R and enter:


To cite this package in a publication, start R and enter:



PDF R Script Analysis examples using phyloseq
PDF R Script Basic data manipulation using phyloseq
PDF phyloseq_classes_4.pdf
PDF   Reference Manual
Text   NEWS


biocViews Classification, Clustering, GeneticVariability, HighThroughputSequencing, MultipleComparisons, QualityControl, Software
Version 1.2.1
In Bioconductor since BioC 2.10 (R-2.15)
License AGPL-3
Depends R (>= 2.15.0), methods, ade4 (>= 1.4), ggplot2 (>= 0.9.2), picante (>= 1.3)
Imports ape (>= 3.0), foreach (>= 1.3), igraph0 (>= 0.5), multtest(>= 2.8), plyr (>= 1.7.1), reshape (>= 0.8.4), RJSONIO (>= 0.98), scales (>= 0.2.2), vegan (>= 2.0)
Suggests genefilter, testthat
System Requirements
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source phyloseq_1.2.1.tar.gz
Windows Binary (32- & 64-bit)
MacOS 10.5 (Leopard) phyloseq_1.2.1.tgz
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