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Table 3 Comparison of tools considering the available layout algorithms Table 3: the table lists the networks layout provided by each tool.

From: Visualization of protein interaction networks: problems and solutions

Layout algorithms Tools
  Arena3D AVIS BioLayout3D Cytoscape Medusa NAViGaTOR ONDEX Osprey Pajek PIVOT ProViz
Simulated Annealing - - - - - - - - ? ?
Tree/Radial - - - - - - - ? ?
Clustering - - - - - - - ? ?
SpringEmbed - - - - - - - - ? ?
Force Directed F F F - K: F ? ?
Hierarchical - - - S - - ? ?
Circular - - ? ?
Grid - - - - - - ? ?
Un/Directed - - - - - - - ? ?
Organic - - - - - - - - ? ?
Random - - - - ? ?
DistanceGeometric - - - - - - - - ? ?
Linear - - - - - - - ? ?
Neighborhood - - - - - - - ? ?
Connectivity - - - - - - - - ? ?
Flip - - - - - - - - ? ?
EigenValues - - - - - - - - ? ?
Un/Weighted - - U/W - U/W - - - - ? ?
  1. In the table cells, F indicates the abbreviation of Fruchterman and Reingold layout algorithm, K indicates the Kamada-Kawa i layout algorithm, S indicates the Sugiyama layout algorithm, U or W indicates Unweighted or Weighted graphs, D or UD indicates directed or undirected graphs. The ? means that it was not possible to establish the feature for the tool.