| name | type | gephi | NetworkX | graphia | cytoscape |
|---|---|---|---|---|---|
| Edge list | tabular | yes | yes | yes | yes |
| Adjacency List | tabular | yes | yes | ||
| Adjacency Matrix | tabular | yes | yes | ||
| GML | text | yes | yes | yes | yes |
| GraphML | xml | yes | yes | yes | yes |
| GEXF | xml | yes | yes | ||
| Pajek NET | tabular | yes | yes | ||
| GraphViz DOT | text | yes | yes | ||
| GDF | tabular | yes | |||
| UCINET DL | text | yes | |||
| Tulip TPL | text | yes | |||
| Netdraw VNA | tabular | yes | |||
| LEDA | yes | ||||
| SparseGraph6 | text | yes | |||
| MatrixMarket | text | yes | |||
| Network Text | text | yes | |||
| Cytoscape Exchange | yes | yes | |||
| JSON Graph | json | yes | |||
| MATLAB data files | yes | ||||
| Biopax OWL | xml | yes | yes | ||
| Cytoscape.js JSON | json | yes | yes | ||
| Simple interaction file | yes | ||||
| Nested network format | yes | ||||
| XGMML | yes | ||||
| SBML | yes |
Not a full list. There is also all variations of RDF: N-Triples, N-Quads, Turtle, TriG and RDF/XML.