Network alignment (NA) can be pairwise (PNA) and multiple (MNA). PNA produces aligned node pairs between two networks, while MNA produces aligned node clusters between more than two networks. Recently, the focus has shifted from PNA to MNA, because MNA captures conserved regions between more networks than PNA (and MNA is thus considered to be more insightful), though at higher computational complexity. The issue is that, due to the different output types of PNA and MNA, a PNA method is only compared to other PNA methods, and an MNA method is only compared to other MNA methods. Comparison of PNA against MNA must be done to evaluate whether MNA’s higher complexity is justified by its higher accuracy.

The PNA vs. MNA evaluation software available on this web page contains source code that was used to calculate alignment quality scores described in the "Pairwise versus multiple global network alignment" paper. PNA vs. MNA evaluation source code, example networks to test this software on, and installation and usage instructions are available for download here.

If you use this software, please reference the following paper: Vipin Vijayan, Eric Krebs, Lei Meng, and Tijana Milenkovic, Pairwise versus multiple global network alignment, under revision, 2018. Also, arXiv:1709.04564 [q-bio.MN].

Vipin Vijayan may be contacted via email at vvijayan [at] nd [dot] edu and Tijana Milenkovic can be contacted via email at tmilenko [at] nd [dot] edu.