Cytoscape
Gephi
Graphviz
KeyLines
UCINET
NodeXL
Pajek
SocNetV
Software AG webMethods
MuleSoft Anypoint Platform
Talend Data Integration
Boomi
Cleo Integration Cloud
Celonis
Zapier
Matillion
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 / 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
Gephi - Gephi is an open-source software for visualizing and analyzing large networks graphs.
MuleSoft Anypoint Platform - Anypoint Platform is a unified, highly productive, hybrid integration platform that creates an application network of apps, data and devices with API-led connectivity.
Graphviz - Graphviz is open source graph visualization software. It has several main graph layout programs.
Talend Data Integration - Talend offers open source middleware solutions that address big data integration, data management and application integration needs for businesses of all sizes.
KeyLines - The JavaScript toolkit for graph visualization
Boomi - The #1 Integration Cloud - Build Integrations anytime, anywhere with no coding required using Dell Boomi's industry leading iPaaS platform.