Table 3

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

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

-

-

-

-

?

?


In the table cells, F indicates the abbreviation of Fruchterman and Reingold layout algorithm, K indicates the Kamada-Kawai 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.

Agapito et al. BMC Bioinformatics 2013 14(Suppl 1):S1   doi:10.1186/1471-2105-14-S1-S1

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