Decomptool version 1.0 manual
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About Decomptool
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Decomptool decomposes biochemical networks into subnetworks based on the
global geometry of the network. The algorithm used by Decomptool is described in [1].

A stoichiometry matrix can be used to input the biochemical network.
Decomptool can read a stoichiometry matrix either from an SBML-file or
from an ASCII matrix file. The ASCII file format is described later in
this file.

The program outputs the decomposed network in the Newick tree format [2].
If an SBML file was used to supply the stoichiometry matrix, the Newick
tree will be labeled with substance names from the file. In case of an
ASCII matrix, the Newick tree will be labeled with integer numbers
starting from 1.

Program usage
=============

Command line parameters:

   -s <string>,  --sbml <string>
        Filename for loading an SBML Reaction Model.

   -m <string>,  --txt <string>
        Filename for loading a stoichiometry matrix.
     
   -o <string>,  --out <string>
        Filename for exporting the Newick clustering tree.
             
   -h,  --help
        Displays usage information and exits.
        
   -v,  --version
        Displays version information and exits.
        
   --quiet
        Print no progress indicators during the calculation

Decomptool will either the '-s' or '-m' parameter, not both.

Description of the ASCII matrix format used by decomptool
=========================================================

<rows><\t><columns>
First line of the file has two integer entries: number of rows and
columns in the matrix.

<\t><entry 1,1><\t><entry 1,2><\t><entry 1,3>
The rest of the lines in the file contain the data, one matrix row in a
file line. Each row begins with one tab-characer( </t> ), and each value
is separated by one tab-character.


References
==========

1. Girvan, M. and Newman, M.E.J. (2002) Community structure in social and
   biological networks. Proc. Natl. Acad. Sci. U.S.A., 99, 7821-7826

2. The Newick tree format:
   http://evolution.genetics.washington.edu/phylip/newicktree.html