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Global Network Alignment using Multiscale Spectral Signatures


GHOST is a software package for global biological network alignment. It computes alignments based on a novel spectral signature for comparing the topological similarity of nodes across networks.


GHOST is developed by Rob Patro, Carl Kingsford at the Lane Center for Computational Biology at Carnegie Mellon University and David Lindenbaum and Kevin Au at the School of Computer Sceience at Carnegie Mellon University.

Please send any questions, comments or bug reports to


User Guide:GHOST User Guide
Data: Data from the paper
Software: GitHub and Linux (x86-64) Binary

Note: the links below point to the no-longer-maintained implemntation of GHOST --- use the links above for the new and more efficient C++ version

Alignment Software: GitHub and source & binary packages
Spectral Signature Extractor: GitHub and source & binary packages


If you make use of GHOST, please cite:

Global network alignment using multiscale spectral signatures
R. Patro and C. Kingsford
Bioinformatics 28 3105--3114 (2012)


EF-0849899, IIS-0812111, CCF-1053918
1R21AI085376, R01HG002945
2008-04049, 2010-15739-01

This material is based upon work supported by the National Science Foundation under Grant Numbers EF-0849899, IIS-0812111, CCF-1053918. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.