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 order
The options -h
are accessible in all clm
modes. They are described in the
clm order [-prefix
<string> (file multiplex
<fname> (concatenated output in single
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.
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 -o
option to specify
the output file. The stacked format can be converted to Newick format using
. The output can be written to multiple files, one for each
projected clustering, by using the -prefix
option. By example,
leads to output in files named P1, P2, ..PN,
where N is the number of clusters in the input, P1 is the most fine-grained
ordered clustering, and PN is the coarsest clustering.
As decribed above.
Stijn van Dongen.
for an overview of all the documentation and the utilities
in the mcl family.