• PhyloNetwork

  • Referenced in 27 articles [sw28216]
  • perl package and an alignment tool for phylogenetic networks. Phylogenetic networks are a generalization ... analysis of phylogenetic networks by computing distances between them or aligning them. Results: In order ... bundle and implements many algorithms on phylogenetic networks. We have also developed a Java applet...
  • IsoRankN

  • Referenced in 10 articles [sw08325]
  • IsoRankN (IsoRank-Nibble), a global multiple-network alignment tool based on spectral clustering ... IsoRankN outperforms existing algorithms for global network alignment in coverage and consistency on multiple alignments...
  • IsoRank

  • Referenced in 10 articles [sw08324]
  • algorithm for global alignment of multiple protein-protein inter- action (PPI) networks. The algorithm aims ... field has focused on local network alignment. The intuition behind our algorithm is that ... input networks and then using k-partite matching to extract the final global alignment across ... compute the first known global alignment of PPI networks from five species: yeast, fly, worm...
  • Graemlin

  • Referenced in 5 articles [sw29736]
  • Graemlin: general and robust alignment of multiple large interaction networks. The recent proliferation of protein ... interaction networks has motivated research into network alignment: the cross-species comparison of conserved functional ... first algorithm capable of scalable multiple network alignment. Græmlin’s explicit model of functional evolution ... developed the first quantitative benchmarks for network alignment, which allow comparisons of algorithms in terms...
  • PathBLAST

  • Referenced in 7 articles [sw29737]
  • protein interaction networks. PathBLAST is 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 ... basic method searches for high-scoring alignments between pairs of protein interaction paths, for which ... interaction pathways based on similarity to the network of another, well-characterized species. PathBLAST...
  • ns-3

  • Referenced in 16 articles [sw09843]
  • open simulation environment for networking research: it should be aligned with the simulation needs...
  • MI-GRAAL

  • Referenced in 3 articles [sw08318]
  • Integrative network alignment reveals large regions of global network similarity in yeast and human. Motivation ... sequence alignment, efficient and reliable network alignment methods are expected to improve our understanding ... biological systems. Unlike sequence alignment, network alignment is computationally intractable. Hence, devising efficient network alignment ... biology. Results: We introduce a novel network alignment algorithm, called Matching-based Integrative GRAph ALigner...
  • GHOST

  • Referenced in 4 articles [sw08322]
  • GHOOST: 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 ... topological similarity of nodes across networks...
  • C-GRAAL

  • Referenced in 3 articles [sw08317]
  • Common-neighbors-based global GRAph ALignment of biological networks. Networks are an invaluable framework ... expected that comparison and alignment of biological networks will have a similar impact ... maximizing the number of aligned edges between two networks and is based solely on network ... networks. We apply C-GRAAL to align PPI networks of eukaryotic and prokaryotic species...
  • NETAL

  • Referenced in 3 articles [sw34152]
  • based method for global alignment of protein–protein interaction networks. Results: We present a novel ... algorithm for the global alignment of protein–protein interaction networks. It uses a greedy method ... networks to find the best global network alignment. NETAL outperforms other global alignment methods ... first server for global alignment of protein–protein interaction networks. Availability: Binaries supported on linux...
  • HubAlign

  • Referenced in 2 articles [sw34150]
  • comparative analysis is to align PPI networks to identify conserved or species-specific subnetwork motifs ... have been developed for global PPI network alignment, but it still remains challenging in terms ... This paper presents a novel global network alignment algorithm, denoted as HubAlign, that makes ... first and gradually extends the alignment to the whole network. Extensive tests indicate that HubAlign...
  • MetNetAligner

  • Referenced in 2 articles [sw25791]
  • service tool for metabolic network alignments. The accumulation of high-throughput genomic, proteomic and metabolical ... accurate modeling and reconstruction of metabolic networks. Alignment of the reconstructed networks can help ... service tool MetNetAligner which aligns metabolic networks, taking in account the similarity of network topology ... identification of enzymes. The tool supports several alignment options including allowing or forbidding enzyme deletion...
  • GEDEVO

  • Referenced in 2 articles [sw08298]
  • graph edit distance algorithm for biological network alignment. With the so-called OMICS technology ... kinds of biological entities. The emerging interaction networks are usually modeled as graphs with thousands ... addition to sequence alignment, the comparison of biological networks has proven great potential to infer ... proteins and genes. However, the corresponding network alignment problem is computationally hard and theoretically intractable...
  • Natalie

  • Referenced in 3 articles [sw08323]
  • tool for pairwise global network alignment [1]. The current version is capable of reading...
  • GREAT

  • Referenced in 1 article [sw18878]
  • GREAT: GRaphlet Edge-based network AlignmenT. Network alignment aims to find regions of topological ... poorly-studied species between aligned network regions. Typically, existing network aligners first compute similarities between ... find a high-scoring alignment (node mapping between the networks) with respect to “node conservation ... from a novel perspective, by aligning optimally edges between networks first in order to improve...
  • NABEECO

  • Referenced in 1 article [sw08321]
  • software tool for solving the network alignment problem. NABEECO stands for Network Alignment with ... called Graph Edit Distance problem. Network Alignment is a computationally hard bioinformatics problem. It aims ... Protein-Protein Interaction (PPI) networks, Network Alignment, finds its applications in the validation of interactions ... given PPI networks. Network Alignment is a novel basis, in addition to DNA and amino...
  • SANA

  • Referenced in 1 article [sw15882]
  • SANA: Simulated Annealing Network Alignment Applied to Biological Networks. The alignment of biological networks ... solved in polynomial time. In contrast, network alignment is NP-hard, meaning optimal solutions ... algorithm used to create them. Every network alignment algorithm consists of two orthogonal components: first ... search algorithm called SANA: Simulated Annealing Network Aligner. We test it on several popular objective...
  • PrimAlign

  • Referenced in 1 article [sw34148]
  • PrimAlign: PageRank-inspired Markovian alignment for large biological networks. Motivation: Cross-species analysis of large ... cellular organizations and functions. Recently, network alignment algorithms have been proposed to predict conserved interactions ... However, high accuracy and scalability of network alignment are still a challenge. Results: We propose ... novel pairwise global network alignment algorithm, called PrimAlign, which is modeled as a Markov chain...
  • L-GRAAL

  • Referenced in 1 article [sw34161]
  • GRAAL: Lagrangian graphlet-based network aligner. Results: We introduce a novel global network alignment tool ... interaction functional conservations, using a novel alignment search heuristic based on integer programming and Lagrangian ... with the state-of-the-art network aligners on the largest available PPI networks from...
  • IGLOO

  • Referenced in 1 article [sw14829]
  • IGLOO: Integrating global and local biological network alignment. Biological network alignment (NA) aims to find ... regions of similarities between molecular networks of different species. NA can be either local ... high functional but low topological alignment quality, while GNA has high topological but low functional...