GraphAlignment: GraphAlignment is an extension package for the R programming environment which provides functions for finding an alignment between two networks based on link and node similarity scores. This package implements the Bayesian scoring methods and the alignment algorithm introduced in the paper J. Berg and M. Lässig, “Cross-species analysis of biological networks by Bayesian alignment”, PNAS 103 (29), 10967-10972 (2006). Documentation and installation guide are available here.

PathBLAST: PathBLAST is a network alignment and search tool for comparing protein interaction networks across species to identify protein pathways and complexes that have been conserved by evolution. PathBLAST is now available at http://www.pathblast.org/ as a web-based query. (publications)

IsoRankN: IsoRankN (IsoRank-Nibble) is a global multiple-network alignment tool based on spectral clustering on the induced graph of pairwise alignment scores. IsoRankN outperforms existing algorithms for global network alignment in coverage and consistency on multiple alignments of the five available eukaryotic networks. Being based on spectral methods, IsoRankN is both error-tolerant and computationally efficient. More information is available here.

NetworkBLAST & NetworkBLAST-M: NetworkBLAST analyzes protein interaction networks across species to infer protein complexes that are conserved in evolution.
For comparing multiple networks use Networkblast-M; for an executable of NetworkBLAST please refer to here.