\name{export_mothur_dist}
\alias{export_mothur_dist}
\title{Export a distance object as \code{.names} and \code{.dist} files for mothur}
\usage{
  export_mothur_dist(x, out=NULL,
  makeTrivialNamesFile=NULL)
}
\arguments{
  \item{x}{(Required). A \code{"dist"} object, or a
  symmetric matrix.}

  \item{out}{(Optional). The desired output filename for
  the \code{.dist} file, OR left \code{NULL}, the default,
  in which case the mothur-formated distance table is
  returned to \code{R} standard out.}

  \item{makeTrivialNamesFile}{(Optional). Default
  \code{NULL}. The desired name of the \code{.names} file.
  If left \code{NULL}, the file name will be a modified
  version of the \code{out} argument.}
}
\value{
  A character vector of the different cutoff values
  contained in the file. For a given set of arguments to
  the \code{cluster()} command from within \emph{mothur}, a
  number of OTU-clustering results are returned in the same
  list file. The exact cutoff values used by \emph{mothur}
  can vary depending on the input data. This simple
  function returns the cutoffs that were actually included
  in the \emph{mothur} output. This an important extra step
  prior to importing the OTUs with the
  \code{import_mothur_otulist()} function.
}
\description{
  The purpose of this function is to allow a user to easily
  export a distance object as a pair of files that can be
  immediately imported by mothur for OTU clustering and
  related analysis. A distance object can be created in
  \code{R} in a number of ways, including via cataloguing
  the cophentic distances of a tree object.
}
\examples{
#
### data(GlobalPatterns)
### myDistObject <- as.dist(cophenetic(tre(GlobalPatterns)))
### export_mothur_dist(myDistObject, "myfilepathname.dist")
}