Table 2 Feature comparison between SNAVI and Cytoscape

• Users can dynamically change the location of nodes

SNAVI: Not available, users have the option to export the network to Pajek or Cytoscape

Cytoscape: Users can move the nodes on the screen

• Different options for network layout

SNAVI: Fixed visualization using presetting of parameters from GraphViz

Cytoscape: Several rendering algorithms for dynamic organization of nodes on the screen

• Coloring of nodes

SNAVI: Can be specified in a text file

Cytoscape: Can be specified dynamically using built-in feature in the software

• Zooming and panning

SNAVI: Offered with some SVG output maps

Cytoscape: Embedded within the main framework

• Computing network statistics

SNAVI: One functions that counts node types, and computes connectivity distribution, characteristic path length, clustering and grid coefficients

Cytoscape: Many network measures for nodes links, and stats for the entire network can be computed with the NetworkAnalyzer plug-in

• Finding and displaying network motifs

SNAVI: Available for only specific types of motifs size 3–5 nodes

Cytoscape: Available using the Metabolica, Network Motif Finder, and NetMatch plug-ins

• Finding paths from source to target

SNAVI: Available with the PathwayGenerator algorithm

Cytoscape: Available with the ShortestPath and PeSca plug-ins

• Generating random networks

SNAVI: Different types of random networks: Erdos-Renyi, Barabasi-Albert, Random Swaps can be created from loaded real networks

Cytoscape: Random Network Plug-in was announced as a Google Summer of Code project

• Linking to background knowledge of protein interactions

SNAVI: Limited to one function that uses a background human protein interaction network

Cytoscape: Can be linked to many different background networks using the BioNetBuilder, BioPAX, MiMI and cPath plug-ins

• Computing network parameters as connectivity propagates through the network

Only in SNAVI implemented specifically for Ma'ayan et al. (1)

• Creating web-sites from networks in text file

Only in SNAVI implemented specifically for Ma'ayan et al. (1)

• Connecting a list of genes using a background network

SNAVI: Limited to one function that uses a background human protein interaction network

Cytoscape: Can be done with several of the plug-ins

• Network clustering using the MCODE plug-in;

Not in SNAVI

Only in Cytoscape

• Linking to microarray data;

• Ability to generate filters; Linking to Gene Ontology with the binGO and GOlorize plug-ins; Linking to domain-domain putative interactions with the DomainNetworkBuilder plug-in; Linking to protein structure; Linking with text mining tools; Network inference algorithms; Ability to merge networks