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Local 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). LNA finds small highly conserved network regions and produces a many-to-many node…
LocalAli
Desktop

LocalAli

A fast and scalable local network alignment tool for the identification of…

A fast and scalable local network alignment tool for the identification of functionally conserved modules in multiple networks. To evaluate the performance and the statistical significance, LocalAli…

LNA_GNA
Desktop

LNA_GNA Local Network Alignment_Global Network Alignment

Evaluates local network alignment (LNA) against global network alignment (GNA).…

Evaluates local network alignment (LNA) against global network alignment (GNA). LNA_GNA method provides guidelines for researchers to properly demonstrate the superiority of a newly proposed network…

MacSyFinder
Web
Desktop

MacSyFinder Macromolecular System Finder

Detects molecular systems in genome data. MacSyFinder identifies the presence…

Detects molecular systems in genome data. MacSyFinder identifies the presence of a given system according to specifications of the input biological model. It determines the presence of a given…

CompNet
Desktop

CompNet

Allows simultaneous visualization and comparison of multiple networks. In…

Allows simultaneous visualization and comparison of multiple networks. In addition to computing generic graph properties for individual networks, CompNet allows multigraph comparisons and similarity…

GraphAlignment
Desktop

GraphAlignment

Permits alignment of vertices that descend from a common ancestor.…

Permits alignment of vertices that descend from a common ancestor. GraphAlignment is based on a hybrid method. It uses an explicit model of network evolution to infer alignment parameters from the…

SiPAN
Desktop

SiPAN SImultaneous Prediction and Alignment of Networks

An algorithm that solves the simultaneous prediction and alignment of networks…

An algorithm that solves the simultaneous prediction and alignment of networks problem in accordance with its simultaneous nature. Bearing the same name as the defined problem itself, the SiPAN…

CUFID-align
Desktop
Corbi
Desktop

Corbi

Provides several tools for bioinformatics analysis. Corbi is an R package that…

Provides several tools for bioinformatics analysis. Corbi is an R package that contains functions for network querying and alignment, subnetwork extraction, search and biomarker identification. The…

tYNA
Web
Desktop

tYNA TopNet-like Yale Network Analyzer

A web system for managing, comparing and mining multiple networks, both…

A web system for managing, comparing and mining multiple networks, both directed and undirected. tYNA provides five main types of functionality: (1) network management: storing, retrieving and…

Isobase
Dataset

Isobase IsoRank PPI Network Alignment Based Ortholog Database

A database identifying functionally related proteins, across five major…

A database identifying functionally related proteins, across five major eukaryotic model organisms: Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, Mus musculus and Homo…

PathBLAST
Web

PathBLAST

A network alignment and search tool for comparing protein interaction networks…

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. The basic method…

NetAligner
Web

NetAligner

A network alignment tool that allows the identification of conserved protein…

A network alignment tool that allows the identification of conserved protein complexes and pathways across organisms, providing valuable hints as to how those interaction networks evolved. NetAligner…

AlignNemo
Desktop

AlignNemo

An algorithm that, given the networks of two organisms, uncovers subnetworks of…

An algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that relate in biological function and topology of interactions. The discovered conserved subnetworks have a…

AlignMCL
Desktop

AlignMCL

Identifies conserved subnetworks in different species using a local alignment…

Identifies conserved subnetworks in different species using a local alignment algorithm. AlignMCL is based on the idea of first merging two protein interaction networks (PINs) in a single alignment…

Netdis
Desktop

Netdis

A topology-based distance measure between networks, which offers the…

A topology-based distance measure between networks, which offers the possibility of network phylogeny reconstruction. Netdis is able to correctly separate different random graph model types…

DualAligner
Desktop

DualAligner

A network alignment algorithm that performs a dual alignment strategy, in which…

A network alignment algorithm that performs a dual alignment strategy, in which both region-to-region alignment and protein-to-protein alignment are performed to achieve superior-quality network…

GASOLINE
Desktop
CNetA
Web

CNetA Conditional Random Fields based Network Alignment Method

A network alignment method based on the conditional random field model. The…

A network alignment method based on the conditional random field model. The method is compared with other four methods on three real protein-protein interaction (PPI) network pairs by using four…

NetworkBLAST-M
Desktop

NetworkBLAST-M

Allows identifying protein complexes in protein-protein interaction (PPI)…

Allows identifying protein complexes in protein-protein interaction (PPI) networks. NetworkBlast-M analyzes networks from multiple species and outputs a set of complexes that are evolutionarily…

NetAlign
Web

NetAlign Network Alignment

A web-based tool designed to enable comparative analysis of protein interaction…

A web-based tool designed to enable comparative analysis of protein interaction networks (PINs). NetAlign compares a query PIN with a target PIN by combining interaction topology and sequence…

CAMPways
Desktop

CAMPways

Provides one-to-many alignments of reactions in a pair of metabolic pathways.…

Provides one-to-many alignments of reactions in a pair of metabolic pathways. When compared with a state-of-the-art alternative, the CAMPways algorithm provides better alignment results on metabolic…

PINALOG
Desktop
Web

PINALOG

A protein-protein interaction networks (PPINs) alignment method which combines…

A protein-protein interaction networks (PPINs) alignment method which combines information from protein sequence, function and network topology. Alignment of human and yeast PPINs reveals several…

NetworkBLAST
Web

NetworkBLAST

The identification of protein complexes is a fundamental challenge in…

The identification of protein complexes is a fundamental challenge in interpreting protein-protein interaction data. Cross-species analysis allows coping with the high levels of noise that are…

NatalieQ
Web

NatalieQ

Molecular interactions need to be taken into account to adequately model the…

Molecular interactions need to be taken into account to adequately model the complex behavior of biological systems. NatalieQ is a web server for aligning two protein-interaction networks in order to…

NAPAbench
Desktop

NAPAbench Network Alignment Performance Assessment Benchmark

A network synthesis model that can generate families of evolutionarily related…

A network synthesis model that can generate families of evolutionarily related synthetic protein-protein interaction (PPI) networks. The proposed model can serve as an effective framework for…

MIMO
Desktop

MIMO Molecular Interaction Maps Overlap

Offers a flexible and efficient graph-matching tool for comparing complex…

Offers a flexible and efficient graph-matching tool for comparing complex biological pathways. The main features of MIMO are: (i) easy-to-use: MIMO takes as input biological networks encoded with the…

VANLO
Desktop

VANLO Visualization of Aligned Networks with Layout Optimization

A visualization system for aligned biological networks in 3D space that…

A visualization system for aligned biological networks in 3D space that naturally embeds existing 2D layouts. VANLO provides an intuitive global understanding of aligned PPI networks and it allows…

SubMAP
Desktop

SubMAP Subnetwork Mappings in Alignment of Pathways

It can identify biologically relevant mappings that are missed by traditional…

It can identify biologically relevant mappings that are missed by traditional alignment methods. SubMAP is scalable for metabolic pathways of arbitrary topology, including searching for a query…

MaWISh
Desktop

MaWISh Maximum Weight Induced Subgraph

A comprehensive alignment tool for PPI networks, which is inspired by…

A comprehensive alignment tool for PPI networks, which is inspired by duplication/divergence models that focus on understanding the evolution of protein interactions. MaWISh is based on a…

PathAligner
Web

PathAligner

A conceptual framework and computational system that allows the retrieval of…

A conceptual framework and computational system that allows the retrieval of metabolic pathway information and the processing of alignments to reveal the similarities between metabolic pathways.…

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