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.SH NAME
clm_order \- reorder clusterings conformal to inclusion structure

clmorder is not in actual fact a program\&. This manual
page documents the behaviour and options of the clm program when
invoked in mode \fIorder\fP\&. The options \fB-h\fP, \fB--apropos\fP,
\fB--version\fP, \fB-set\fP, \fB--nop\fP are accessible
in all \fBclm\fP modes\&. They are described
in the \fBclm\fP manual page\&.
.SH SYNOPSIS

\fBclm order\fP
\fB[-prefix\fP <string> (\fIfile multiplex prefix\fP)\fB]\fP
\fB[-o\fP <fname> (\fIconcatenated output in single file\fP)\fB]\fP
<cluster|stack>+
.SH DESCRIPTION

Given a set of input clusterings \fBclm order\fP 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\&.

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 \fB-o\fP option to
specify the output file\&. The stacked format can be converted to Newick
format using \fBmcxdump(1)\fP\&. The output can be written to multiple files,
one for each projected clustering, by using the \fB-prefix\fP option\&. By
example, \fB-prefix\fP\ \&\fBP\fP leads to output in files named \fCP1\fP, \fCP2\fP,
\&.\&.\fCPN\fP, where \fCN\fP is the number of clusters in the input, \fCP1\fP is the
most fine-grained ordered clustering, and \fCPN\fP is the coarsest clustering\&.
.SH OPTIONS

.ZI 2m "\fB-prefix\fP (\fI<string>\fP)"
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.ZI 2m "\fB-o\fP (\fI<fname>\fP)"
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As decribed above\&.
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.SH AUTHOR

Stijn van Dongen\&.
.SH SEE ALSO

\fBmclfamily(7)\fP for an overview of all the documentation
and the utilities in the mcl family\&.