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GraphML is an XML-based file format for graphs. The GraphML file format results from the joint effort of the graph drawing community to define a common format for exchanging graph structure data. It uses an XML-based syntax and supports the entire range of possible graph structure constellations including directed, undirected, mixed graphs ...
Tulip (software) is a free software in the domain of information visualisation capable of manipulating huge graphs (with more than 1.000.000 elements). yEd, a free Java-based graph editor, supports import from and export to GML. The Graphviz project includes two command-line tools (gml2gv and gv2gml) that can convert to and from the DOT file ...
igraph can be used to generate graphs, compute centrality measures and path length based properties as well as graph components and graph motifs. It also can be used for degree-preserving randomization. igraph can read and write file formats such as Pajek, GraphML, LGL, NCOL, DIMACS, and GML, as well as simple edge lists. [12]
NodeXL Pro imports UCINet and GraphML files, as well as Excel spreadsheets containing edge lists or adjacency matrices, into NodeXL workbooks. NodeXL Pro also allows for the quick collection of social media data via a set of import tools which can collect network data from e-mail, Twitter, YouTube, and Flickr.
Graphviz (short for Graph Visualization Software) is a package of open-source tools initiated by AT&T Labs Research for drawing graphs (as in nodes and edges, not as in bar charts) specified in DOT language scripts having the file name extension "gv". It also provides libraries for software applications to use the tools.
Directed Graph Markup Language (DGML) is an XML-based file format for directed graphs. [1] Introduction to DGML
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Free, CPL? Cross-platform - Mac, Windows, Linux Official website: interactive Tree Of Life (iTOL) No No ? Phylogenetic tree viewer-annotation tool which can visualise alignments directly on the tree. Various other dataset types can be displayed in addition to alignments. FASTA Proprietary, free use Yes Browser Official website: IVisTMSA No