MetaPAT: A Tool for the Alignment of Metabolic Pathways


From this page you can download an alignment tool for metabolic networks as described in

  • S. Wernicke and F. Rasche.
    Simple and fast alignment of metabolic pathways by exploiting local diversity.  PDF  Bioinformatics.
    Accepted for publication, April 2007.


You may use MetaPAT for all of your research purposes as long as you do the following:

  • You acknowledge its use in any published work that fully or in part derives its results from its usage. (If you wish to make a bibliographical reference, please consider citing the above article for that purpose.)
  • You do not sell anything that is based on or derived from it.

Absolutely no guarantees or warranties are made concerning the suitability, correctness, or any other aspect of the distributed files. Any use is at your own risk. This software uses the GraphViz library version 2.12 by Stephen North et al.


Last updated on February 15th, 2007.

  Linux logo

Download zipped executable for Linux (GTK/i386) here.

  Windows logo

Download zipped executable for 32-bit Windows (i386) here.
The Windows version is preliminary in that the graph Layout is not yet working, but the core algorithm works fine.

  Documentation logo

Download the documentation here.

Some testdata is available from the BioCyc webpage.


The program was written by Florian Rasche (email) in collaboration with Sebastian Wernicke (homepage, email). Sebastian Wernicke's research was funded by a scholarship from the Deutsche Telekom Stiftung. Florian Rasche's position as a student research assistant is funded by the Deutsche Forschungsgemeinschaft, project PEAL (Parameterized Complexity and Exact Algorithms), NI 369/1.

 Deutsche Telekom Stiftung          German National Academic Foundation 


Happy graph aligning!

Florian Rasche (email)
Jena, February 15th, 2007.