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 | - | - | - | - | ? | ? |