Cytoscape
Gephi
Graphviz
KeyLines
UCINET
NodeXL
Pajek
SocNetV
OrientDB
ArangoDB
neo4j
Redis
Azure Cosmos DB
MongoDB
Apache Cassandra
CouchBase
Cytoscape OrientDBNo features have been listed yet.
Based on our record, Cytoscape seems to be a lot more popular than OrientDB. While we know about 11 links to Cytoscape, we've tracked only 1 mention of OrientDB. 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 / 4 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
First, you need to choose a specific graph database platform to work with, such as Neo4j, OrientDB, JanusGraph, Arangodb or Amazon Neptune. Once you have selected a platform, you can then start working with graph data using the platform's query language. - Source: dev.to / about 1 year ago
Gephi - Gephi is an open-source software for visualizing and analyzing large networks graphs.
ArangoDB - A distributed open-source database with a flexible data model for documents, graphs, and key-values.
Graphviz - Graphviz is open source graph visualization software. It has several main graph layout programs.
neo4j - Meet Neo4j: The graph database platform powering today's mission-critical enterprise applications, including artificial intelligence, fraud detection and recommendations.
KeyLines - The JavaScript toolkit for graph visualization
Redis - Redis is an open source in-memory data structure project implementing a distributed, in-memory key-value database with optional durability.
