GRAAL (GRAph ALigner) Algorithm

Supplementary Information for: "Topological network alignment uncovers biological function and phylogeny"

Oleksii Kuchaiev*, Tijana Milenkovic*, Vesna Memisevic, Wayne Hayes, Natasa Przulj
* These authors contributed equally to this work

Corresponding author: Prof. Natasa Przulj, e-mail: natasa [AT]

Download GRAAL

How to run GRAAL:

  • GRAAL has been tested on Gentoo and Mandriva Linux distributions.
    However, it should work with other distributions.
  • Download and unpack the GRAAL using the link above.
  • GRAAL accepts networks in LEDA .gw format.
  • Your should have Python installed on your system
  • Run "./" without any parameters and it will display usage directions
  • Number of nodes in the first network must not be greater than number
    of nodes in the second network

Sample Usage:

  • Go to the directory where you unpacked GRAAL.
  • In terminal type "./ 0.8 result"

How to convert network from edge list format to .gw file accepted by GRAAL:

If your network is in edge list format:

node1 node2
node3 node4

You can use "list2leda" script (part of to convert it into the format accepted by GRAAL.
Use it like this: "./list2leda edgelist.txt >>"
Note that self-loops, directionality and double edges will be ignored.