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Global network alignment software tools | Pathway analysis

Network alignment (NA) aims to find regions of similarities between species’ molecular networks. There exist two NA categories: local (LNA) and global (GNA). GNA finds large conserved regions and produces a one-to-one node mapping. Source…
NetCoffee
Desktop

NetCoffee

Allows to find a global alignment of multiple protein-protein interaction…

Allows to find a global alignment of multiple protein-protein interaction networks. NetCoffee searches for a global alignment by maximizing a target function using simulated annealing on a set of…

NETAL
Desktop
Web

NETAL Network Alignment

An algorithm for the global alignment of protein-protein interaction networks.…

An algorithm for the global alignment of protein-protein interaction networks. NETAL uses a greedy method, based on the alignment scoring matrix, which is derived from both biological and topological…

SMAL
Web

SMAL Scaffold-Based Multiple Network Aligner

A public, open-source, web-based application for determining multiple network…

A public, open-source, web-based application for determining multiple network alignments (MNAs) from existing pairwise network alignments (PNAs) that addresses all the aforementioned challenges. With…

C3Part/Isofun
Desktop

C3Part/Isofun

Allows alignment between two or more graphs of biological data. C3Part/Isofun…

Allows alignment between two or more graphs of biological data. C3Part/Isofun is a versatile tool to study syntenies in bacteria, that may be adapted to various kinds of studies such as genomes,…

SANA
Web

SANA Simulated Annealing Network Aligner

Explores the space of alignments looking for ones scoring well according to M…

Explores the space of alignments looking for ones scoring well according to M (an objective function for alignment quality). SANA is based on a metaheuristic search algorithm with a rich history of…

multiMAGNA++
Desktop

multiMAGNA++

Maximizes an alignment quality measure by evolving a population of alignments…

Maximizes an alignment quality measure by evolving a population of alignments over time. multiMAGNA++ can be used for biological network alignment, i.e., to align molecular networks of different…

ModuleAlign
Desktop

ModuleAlign

A method for pairwise global alignment of protein–protein interaction (PPI)…

A method for pairwise global alignment of protein–protein interaction (PPI) networks. Its novel scoring scheme integrates sequence information and both local and global network topology. Based on a…

Fuse
Desktop

Fuse

A global multiple network aligner. First, Fuse computes novel similarity scores…

A global multiple network aligner. First, Fuse computes novel similarity scores between proteins by fusing sequence similarities and network wiring patterns over all proteins in all PPI networks…

CytoGEDEVO
Desktop

CytoGEDEVO Graph Edit Distance + EVOlution

A Cytoscape app for visual and user-assisted network alignment. CytoGEDEVO…

A Cytoscape app for visual and user-assisted network alignment. CytoGEDEVO extends the previous GEDEVO methodology for global pairwise network alignments with new graphical and functional features.…

CytoMCS
Desktop

CytoMCS

Computes the maximum common edge subgraph problem for two or more graphs.…

Computes the maximum common edge subgraph problem for two or more graphs. CytoMCS is a heuristic maximum common edge subgraph detection tool for the Cytoscape network analysis and visualization…

L-GRAAL
Desktop

L-GRAAL Lagrangian GRAphlet-based network Aligner

A global network alignment tool, which combines an efficient solver based on…

A global network alignment tool, which combines an efficient solver based on Lagrangian relaxation with a scoring function based on the statistics of small induced subgraphs called graphlets. Unlike…

MAGNA++
Desktop

MAGNA++

It is an extension of MAGNA. MAGNA++ introduces several novelties: 1) It…

It is an extension of MAGNA. MAGNA++ introduces several novelties: 1) It simultaneously maximizes any one of three different measures of edge conservation (including our recent superior S3 measure)…

Optnetalign
Desktop

Optnetalign

A multiobjective memetic algorithm for the problem of PPI network alignment…

A multiobjective memetic algorithm for the problem of PPI network alignment that uses extremely efficient swap-based local search, mutation, and crossover operations to create a population of…

GraphCrunch
Desktop

GraphCrunch

Finds well-fitting network models by comparing large real-world networks…

Finds well-fitting network models by comparing large real-world networks against random graph models according to various network structural similarity measures. GraphCrunch has unique capabilities…

Graemlin
Desktop
Web

Graemlin

Algorithm capable of scalable multiple network alignment. Graemlin's…

Algorithm capable of scalable multiple network alignment. Graemlin's explicit model of functional evolution allows both the generalization of existing alignment scoring schemes and the location…

SUMONA
Desktop

SUMONA Supervised Method for Optimizing Network Alignment

Provides an improvement over the OptNetAlign methodology. SUMONA main…

Provides an improvement over the OptNetAlign methodology. SUMONA main contribution is increasing the performance of achieving multiple alignment objectives by supervising the optimization process and…

HubAlign
Desktop

HubAlign

A global network alignment algorithm that makes use of both network topology…

A global network alignment algorithm that makes use of both network topology and sequence homology information, based upon the observation that topologically important proteins in a PPI network…

MAGNA
Desktop

MAGNA Maximizing Accuracy in Global Network Alignment

A program to directly "optimize" edge conservation while the…

A program to directly "optimize" edge conservation while the alignment is constructed, without decreasing the quality of node mapping. MAGNA uses a genetic algorithm and a novel function…

BEAMS
Desktop

BEAMS

A formal definition of the global many-to-many alignment of multiple…

A formal definition of the global many-to-many alignment of multiple protein-protein interaction networks. The computational burden of the BEAMS algorithm in terms of execution speed and memory…

WAVE
Desktop

WAVE Weighted Alignment VotEr

Provides a general network alignment strategy for simultaneously optimizing…

Provides a general network alignment strategy for simultaneously optimizing both node conservation and weighted edge conservation. WAVE can be used with any node cost function or combination of…

NABEECO
Desktop

NABEECO Network Alignment with BEE Colony Optimization

Utilizes the artificial bee colony computing strategies for solving the…

Utilizes the artificial bee colony computing strategies for solving the so-called Graph Edit Distance (GED) problem. NABEECO is a tool for protein-protein interaction (PPI) network alignment. It is a…

GHOST
Desktop

GHOST

A global pairwise network aligner that uses a novel spectral signature to…

A global pairwise network aligner that uses a novel spectral signature to measure topological similarity between subnetworks. GHOST combines a seed-and-extend global alignment phase with a local…

IsoRankN
Desktop

IsoRankN IsoRank-Nibble

A global multiple-network alignment tool based on spectral clustering on the…

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…

MI-GRAAL
Desktop

MI-GRAAL Matching-based Integrative GRAph ALigner

A network alignment algorithm which can integrate any number and type of…

A network alignment algorithm which can integrate any number and type of similarity measures between network nodes (e.g. proteins), including, but not limited to, any topological network similarity…

PISwap
Desktop

PISwap

An algorithm for optimizing global pairwise alignments of protein interaction…

An algorithm for optimizing global pairwise alignments of protein interaction networks, based on a local optimization heuristic that has previously demonstrated its effectiveness for a variety of…

SPINAL
Desktop

SPINAL

Given protein-protein interaction (PPI) networks of a pair of species, a…

Given protein-protein interaction (PPI) networks of a pair of species, a pairwise global alignment corresponds to a one-to-one mapping between their proteins. SPINAL is an algorithm for the problem…

SMETANA
Desktop
Natalie
Desktop

Natalie

Calculates global pairwise network alignment. Natalie is a Lagrangian…

Calculates global pairwise network alignment. Natalie is a Lagrangian relaxation approach that, in combination with a branch-and-bound method, computes provably optimal network alignments.…

HopeMap
Desktop

HopeMap

A connected-components based fast algorithm for network alignment. Comparing to…

A connected-components based fast algorithm for network alignment. Comparing to existing tools, HopeMap is fast with linear computational cost, highly accurate in terms of KO and GO terms specificity…

SIGNALIGN
Web

SIGNALIGN

Aligns pathways using integrated database information from SCOP, CATH, EC…

Aligns pathways using integrated database information from SCOP, CATH, EC number and UniProt. SIGNALIGN is a web-based tool which provides a search engine. This search engine mines the related…

IsoRank
Desktop

IsoRank

An algorithm for global alignment of multiple protein-protein interaction (PPI)…

An algorithm for global alignment of multiple protein-protein interaction (PPI) networks. The guiding intuition here is that a protein in one PPI network is a good match for a protein in another…

C-GRAAL
Desktop

C-GRAAL Common-neighbors based GRAph ALigner

Uses heuristics for maximizing the number of aligned edges between two networks…

Uses heuristics for maximizing the number of aligned edges between two networks and is based solely on network topology. As such, it can be applied to any type of network, such as social,…

AbiNet
Web

AbiNet

Allows users to align and query biological networks. AbiNet matches connected…

Allows users to align and query biological networks. AbiNet matches connected subgraphs to proceed. It constructs a one-to-one correspondence between pairs of nodes in the two networks. This tool can…

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