GRAAL (GRAph ALigner) Algorithm

Supplementary information for "Topological network alignment uncovers biological function and phylogeny"

Oleksii Kuchaiev*, Tijana Milenković*, Vesna Memišević, Wayne Hayes and Nataša Pržulj

_{* These authors contributed equally to this work}

Corresponding author: Prof. N. Pržulj, natasa.przulj@mbzuai.ac.ae

Downloads

• Download GRAAL
• Supplementary information: Supplementary Information and Supplementary Tables 1–8, as one zip file

How to run GRAAL

• GRAAL has been tested on Gentoo and Mandriva Linux, but should work on other distributions.
• Download and unpack GRAAL using the link above.
• GRAAL accepts networks in LEDA .gw format.
• You need Python installed.
• Run ./GRAALRunner.py without parameters to see usage directions.
• The number of nodes in the first network must not be greater than the number of nodes in the second network.

Example

In the folder where you unpacked GRAAL:

./GRAALRunner.py 0.8 testGraph1.gw testGraph2.gw result

Converting an edge list to .gw

If your network is an edge list:

node1 node2
node3 node4
...

convert it with the list2leda script included in the GRAAL download:

./list2leda edgelist.txt >> graph.gw

Self-loops, edge directions and duplicate edges are ignored.

Citation

O. Kuchaiev, T. Milenković, V. Memišević, W. Hayes and N. Pržulj. Topological network alignment uncovers biological function and phylogeny. Journal of the Royal Society Interface 7(50), 1341–1354 (2010). https://doi.org/10.1098/rsif.2010.0063