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Protein similarity network generation software tools | Pathway analysis

Protein similarity networks are graphical representations of sequence, structural and other similarities among proteins for which pairwise all-by-all similarity connections have been calculated. Mapping of biological and other information to network…
EFI-EST
Web

EFI-EST Enzyme Function Initiative-Enzyme Similarity Tool

Facilitates analysis of sequence function space in enzyme families using…

Facilitates analysis of sequence function space in enzyme families using sequence similarity networks (SSNs). EFI-EST is a web-server that generates SSNs in a predominately automated manner. The…

CompositeSearch
Desktop

CompositeSearch

Detects composite gene families in large data sets. CompositeSearch is a…

Detects composite gene families in large data sets. CompositeSearch is a program allowing identification of composite gene families in the range of several million sequences. This tool assists users…

MOCASSIN-prot
Desktop

MOCASSIN-prot

Serves for protein classification. MOCASSIN-prot utilizes quantitative sequence…

Serves for protein classification. MOCASSIN-prot utilizes quantitative sequence similarity information from all domains on the proteins and builds a network that houses clusters of similar protein…

Pythoscape
Desktop

Pythoscape

Creates and manages protein similarity networks. Pythoscape provides several…

Creates and manages protein similarity networks. Pythoscape provides several options to calculate pairwise similarities for input sequences or structures, applies filters to network edges and defines…

NetComm
Desktop

NetComm

Provides a degree-normalized network connectedness metric inspired by network…

Provides a degree-normalized network connectedness metric inspired by network communicability and suitable for analysis of large complex networks. NetComm is an implementation of this method for the…

PANADA
Web
Desktop

PANADA Protein Association Network Annotation Determination and Analysis

Generates protein similarity networks to be used with Cytoscape. PANADA allows…

Generates protein similarity networks to be used with Cytoscape. PANADA allows the user to either automatically search similar sequences or to generate a network with a set of selected proteins. The…

MosaicFinder
Desktop

MosaicFinder

Gathers composite and component gene families and reduces the risk of…

Gathers composite and component gene families and reduces the risk of outputting a large number of false positives. MosaicFinder is based on the graph theoretic tool of clique separator…

SCPS
Desktop

SCPS Spectral Clustering of Protein Sequences

Allows users to detect many of the family/superfamily relationships. SCPS…

Allows users to detect many of the family/superfamily relationships. SCPS provides an implementation of the spectral clustering algorithm requiring no background knowledge in programming or in the…

TRIBE-MCL
Algorithm

TRIBE-MCL

Generates accurate protein families using the Markov Cluster (MCL) formalism…

Generates accurate protein families using the Markov Cluster (MCL) formalism for graph clustering by flow simulation. TRIBE-MCL is an algorithm that allows the efficient and rapid clustering of any…

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