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Cytoscape
Gephi
KeyLines
Graphviz
UCINET
NodeXL
SocNetV
Pajek
Othello
Ticket to Ride
Puzzle Strike
Streets of Chaos
Lux Delux
Tic Tac Toe
MindFeud
Carrom 3D
CytoscapeBased on our record, Cytoscape seems to be more popular. It has been mentiond 11 times since March 2021. We are tracking product recommendations and mentions on various public social media platforms and blogs. They can help you identify which product is more popular and what people think of it.
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 / 6 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
Gephi - Gephi is an open-source software for visualizing and analyzing large networks graphs.
Ticket to Ride - Ticket to Ride is a Turn-based Strategy, Puzzle, Board, Co-op, Single, and Multiplayer video game created and published by Days of Wonder and Asmodee Digital.
KeyLines - The JavaScript toolkit for graph visualization
Puzzle Strike - Puzzle Strike is a Puzzle, Board, Single and Multiplayer video game created and published by Sirlin Games.
Graphviz - Graphviz is open source graph visualization software. It has several main graph layout programs.
Streets of Chaos - Streets of Chaos is a Puzzle, Tactical, Turn-based Strategy and Single-player Simulation created by SimProse Studios.