clmorder.azm

\import{mcx.zmm}

\begin{pud::man}{

   {name}{clm order}
   {html_title}{The clm order manual}
   {author}{Stijn van Dongen}
   {section}{1}
   {synstyle}{long}
   {defstyle}{long}

   \man_share
}

\${html}{\"pud::man::maketoc"}

\sec{name}{NAME}
\NAME{clm order}{reorder clusterings conformal to inclusion structure}

\disclaim_clm{order}

\sec{synopsis}{SYNOPSIS}
\par{
   \clm{order}
   \synoptopt{-prefix}{<string>}{file multiplex prefix}
   \synoptopt{-o}{<fname>}{concatenated output in single file}
   <cluster|stack>+
   }

\sec{description}{DESCRIPTION}

\par{
   Given a set of input clusterings \clm{order} first transform it into a stack
   of strictly nesting clusterings. It does this by splitting clusters where
   necessary.

   It then reorders the coarsest (i.e. level-one) clustering, from large to
   small clusters.  After that it reorders the second coarsest clustering
   conformally such that the first batch among its reordered clusters covers the
   level-one largest cluster, the second batch covers the level-one second
   largest cluster, and so on.  Within these constraints, each batch of
   second-level clusters (corresponding to a single first-level cluster) is
   again ordered from larger to smaller clusters.  This process is applied
   recursively throughout the entire stack of input clusters.
   }

\par{
   The input can be specified in multiple files, and a single file may contain
   multiple clusterings. The output is by default written as a concatenation of
   matrix files, the so-called stack format.  Use the \genopt{-o} option to
   specify the output file.  The stacked format can be converted to Newick
   format using \mysib{mcxdump}.  The output can be written to multiple files,
   one for each projected clustering, by using the \genopt{-prefix} option.  By
   example, \useopt{-prefix}{P} leads to output in files named \v{P1}, \v{P2},
   ..\v{PN}, where \v{N} is the number of clusters in the input, \v{P1} is the
   most fine-grained ordered clustering, and \v{PN} is the coarsest clustering.
   }

\sec{options}{OPTIONS}


\'begin{itemize}{\mcx_itemopts}

\items{
{\defopt{-prefix}{<string>}}
{\defopt{-o}{<fname>}}
}
\car{
   As decribed above.
   }

\'end{itemize}


\sec{author}{AUTHOR}
\par{
   Stijn van Dongen.
   }

\sec{seealso}{SEE ALSO}

\par{
   \mysib{mclfamily} for an overview of all the documentation
   and the utilities in the mcl family.
   }

\end{pud::man}