\docType{package}
\name{phyloseq-package}
\alias{phyloseq-package}
\title{Handling and analysis of high-throughput phylogenetic sequence data.}
\description{
  There are already several ecology and phylogenetic
  packages available in R, including the adephylo, vegan,
  ade4, picante, ape, phangorn, phylobase, and OTUbase
  packages. These can already take advantage of many of the
  powerful statistical and graphics tools available in R.
  However, prior to \emph{phyloseq} a user must devise
  their own methods for parsing the output of their
  favorite OTU clustering application, and, as a
  consequence, there is also no standard within
  Bioconductor (or R generally) for storing or sharing the
  suite of related data objects that describe a
  phylogenetic sequencing project. The phyloseq package
  seeks to address these issues by providing a related set
  of S4 classes that internally manage the handling tasks
  associated with organizing, linking, storing, and
  analyzing phylogenetic sequencing data. \emph{phyloseq}
  additionally provides some convenience wrappers for input
  from common clustering applications, common analysis
  pipelines, and native implementation of methods that are
  not available in other R packages.
}
\author{
  Paul J. McMurdie II \email{mcmurdie@stanford.edu}
}
\references{
  \url{www.stanford.edu/~mcmurdie}
}
\keyword{package}