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Network motif identification software tools | Pathway analysis

Network motif detection is the search for statistically overrepresented subgraphs present in a larger target network. They are thought to represent key structure and control mechanisms. Although the problem is exponential in nature, several…
gtrieScanner
Desktop

gtrieScanner

A software tool that uses the g-trie data structure to count occurrences of…

A software tool that uses the g-trie data structure to count occurrences of subgraphs on larger graphs, determining if they are network motifs. To compile you need a C++ compiler (use GCC if…

ISMAGS
Desktop

ISMAGS Index-based Subgraph Matching Algorithm with General Symmetries

Enumerates all instances of a motif in a graph, making optimal use of the…

Enumerates all instances of a motif in a graph, making optimal use of the motif’s symmetries to make the search more efficient. The ISMAGS algorithm is able to enumerate all instances of a motif…

MOTUS
Desktop

MOTUS

Enables generation of hypotheses on the evolution of metabolic pathways. MOTUS…

Enables generation of hypotheses on the evolution of metabolic pathways. MOTUS also analyzes some global features of the whole network. It uses the reaction graph as model for the metabolic network.…

DCD
Desktop

DCD Differential Community Detection

Identify differential sub-networks as differential communities in a de-noised…

Identify differential sub-networks as differential communities in a de-noised version of the different topological (DT) graph. DCD can (i) iteratively re-order the nodes of the DT graph to determine…

NetExplore
Desktop
Web

NetExplore

Provides options for network design. A user defines the number of network…

Provides options for network design. A user defines the number of network components, order and sign of regulatory links between the components. NetExplore allows plotting and visualization of the…

WaRSwap
Desktop

WaRSwap

A randomization algorithm that for the first time provides a practical network…

A randomization algorithm that for the first time provides a practical network motif discovery method for large multi-layer networks, for example those that include transcription factors, microRNAs,…

FANMOD
Desktop

FANMOD

A tool for fast network motif detection. FANMOD relies on recently developed…

A tool for fast network motif detection. FANMOD relies on recently developed algorithms to improve the efficiency of network motif detection by some orders of magnitude over existing tools. This…

mfinder
Desktop

mfinder

Allows estimation of subgraph concentrations and detection of network motifs at…

Allows estimation of subgraph concentrations and detection of network motifs at a runtime that is asymptotically independent of the network size. mfinder is based on random sampling of subgraphs.…

NetMODE
Desktop

NetMODE

A network motif detection package. NetMODE also (a) includes a method for…

A network motif detection package. NetMODE also (a) includes a method for generating comparison graphs uniformly at random, (b) can interface with external packages (e.g. R), and (c) can utilize…

acc-MOTIF
Desktop

acc-MOTIF

A free software tool to detect network motifs os size 3, 4 and 5. It is…

A free software tool to detect network motifs os size 3, 4 and 5. It is implemented in Java. acc-MOTIF is based in a recent combinatorial approach to accelerate motif detection.

Kavosh
Desktop

Kavosh

An algorithm for finding k-size network motifs with less memory and CPU time in…

An algorithm for finding k-size network motifs with less memory and CPU time in comparison to other existing algorithms. Kavosh is based on counting all k-size sub-graphs of a given graph (directed…

MAVisto
Desktop

MAVisto

A tool for the exploration of motifs in network. MAVisto provides a flexible…

A tool for the exploration of motifs in network. MAVisto provides a flexible motif search algorithm and different views for the analysis and visualisation of network motifs. It is written in Java and…

QuateXelero
Desktop

QuateXelero

Provides a fast motif detection algorithm which has a Quaternary Tree data…

Provides a fast motif detection algorithm which has a Quaternary Tree data structure in the heart. QuateXelero is especially fastest in constructing the central data structure of the algorithm from…

MODA
Desktop

MODA

An algorithm that incorporates techniques such as a pattern growth approach for…

An algorithm that incorporates techniques such as a pattern growth approach for extracting larger motifs efficiently. While most of the algorithms rely on induced subgraphs as motifs of the networks,…

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