Doing a bit more digging, it's using cytoscape[0] which is similar to graphviz. If you search your favorite search engine with "Cytoscape Session Viewer", you'll find many websites displaying the same type of graphs (select layout: circle). FYI, circo doesn't always output a circle. I recently created https://github.com/MegaManSec/SSH-Snake/blob/main/tools/SSH-Snake-dot-circo.png. - Source: Hacker News / 5 months ago

The YAML files are then parsed, and a CYJS file produced, which is a graph model. This is used directly in the web app, but can also be opened in the Cytoscape desktop app , and imported into Neo4j if desired. I can add additional "export" steps to the automated build process, so e.g. GraphML (yEd, Gephi) or DOT files (GraphViz, mermaid, etc) can be used for whatever purpose needed. Source: about 1 year ago

Both Cytoscape and Gephi are options that you can try on Windows; both can run some classic community detection algorithms and can be extended with plugins. Personally, I'd recommend you to use igraph, which can be run as an R or python libraries. Then, about the specific algorithm, I have no experience on amino acid communities, but I would approach the issue thinking the properties that you would like to... Source: over 1 year ago

Two common GUI tools for analysis and editing of graph data are Gephi and Cytoscape. An older alternative starting with a P is Pajek, but I've never used it. Source: almost 2 years ago

I've been thinking that Gephi is getting long in the tooth. Has anybody tried Cytoscape? (https://cytoscape.org/) (DNS is SERVFAILing at the moment.) I use it for a combination of "no K" clustering (general exploration) and what's referred to in threat intelligence by the term of art "pivoting". - Source: Hacker News / about 2 years ago

Some Python libraries have a C/C++ core that relies on libraries such as Cairo and Boost and many others. Such dependencies are not installable with pip/venv simply because they are not Python packages. If you want to try one example, have a go on installing Graph-Tool using pip. Source: over 1 year ago

Do they offer the full feature set of graph-tools? https://graph-tool.skewed.de/. Source: over 1 year ago

Graph-tool - it does only 2D plots and has very slow interactive graphs. Source: about 2 years ago

Graph-tool: This is the one I use the least, although it is probably one of the most powerful. It lets you quickly run advanced community detection analyses like stochastic block models, hierarchical partitions, etc. It also has a fantastic visualization suite for making gorgeous figures. It used to be a pain in the ass to compile, which is why I ended up sinking the time into igraph, although I understand that... Source: about 3 years ago