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: Reddit / 5 months 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: Reddit / 9 months 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 / 12 months ago
The formatting stuff was all in Cytoscape, which is a pretty sick program for graph stuff. - Source: Reddit / about 1 year ago
Protein interaction networks: Cytoscape. - Source: Reddit / over 1 year ago
Have you had a look at Cytoscape? I think this could work for what you're doing. It has a lot of layout options https://cytoscape.org. - Source: Reddit / over 1 year ago
Also if you don't need to embed it in a webpage you can just use cytoscape. - Source: Reddit / over 1 year ago
What about this one? https://cytoscape.org/. - Source: Reddit / almost 2 years ago
Hi! I'm looking for software that can map biological pathways and from several posts I found on ReasearchGate and Biostars, it seems like Cytoscape and PathVisio are the major players here. So I want to know what is the differences and which might be better for my need. PathVisio claimed that these are very different programs and it also mentioned that "PathVisio sees pathways as drawings, not as graphs. This... - Source: Reddit / almost 2 years ago
Do you know an article comparing Cytoscape to other products?
Suggest a link to a post with product alternatives.