Cytoscape VS Apache TinkerPop

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: 12 months 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

The API for Gremlin is built based on Apache TinkerPop, a graph computing framework that uses the Gremlin query language. - Source: dev.to / 20 days ago

You might take a look at Tinkerpop: https://tinkerpop.apache.org/. - Source: Hacker News / 3 months ago

Property Graph, mainly represented as node and relationship in which they can have properties. The database for this kind of data is usually called Graph Database. Gremlin - by TinkerPop project and Cypher - by Neo4J are their query language (also AQL - Arango Query Language - by ArangoDB, but AQL does not only provides graph query language). - Source: dev.to / over 2 years ago

The most common graph query language at the moment would be Gremlin, which is part of the Apache TinkePop graph computing framework. It is simple to write, easy to learn, and widely supported by many graph databases and even non-graph databases that can emulate graph queries. On the other hand, it can be verbose for long queries but generally works well for both OLTP and analysis work. - Source: dev.to / almost 3 years ago