Software Alternatives & Reviews

Cytoscape VS Gephi

Compare Cytoscape VS Gephi and see what are their differences

Cytoscape logo Cytoscape

Cytoscape Official Web Site

Gephi logo Gephi

Gephi is an open-source software for visualizing and analyzing large networks graphs.
  • Cytoscape Landing page
    Landing page //
    2021-07-29
  • Gephi Landing page
    Landing page //
    2022-01-18

Cytoscape

Categories
  • Diagrams
  • Flowcharts
  • Network & Admin
  • Data Visualization
Website cytoscape.org
Details $-

Gephi

Categories
  • Diagrams
  • Flowcharts
  • Wireframing
  • Flow Charts And Diagrams
Website gephi.org
Details $

Cytoscape videos

Cytoscape Tutorial- Beginners Guide in Jupyter

More videos:

  • Review - MetScape App for Cytoscape: Creating and Viewing Correlation Networks
  • Review - Download a Sequence Similarity Network from the EFI, import it into Cytoscape and apply a layout

Gephi videos

Basics of Scientific Literature Analysis, Part 4: Network analysis/visualization with Gephi

More videos:

  • Tutorial - Gephi Tutorial - How to use Gephi for Network Analysis
  • Tutorial - Gephi Tutorial on Network Visualization and Analysis

Category Popularity

0-100% (relative to Cytoscape and Gephi)
Diagrams
35 35%
65% 65
Flowcharts
39 39%
61% 61
Data Visualization
44 44%
56% 56
Graph Visualization
30 30%
70% 70

User comments

Share your experience with using Cytoscape and Gephi. For example, how are they different and which one is better?
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Social recommendations and mentions

Based on our record, Gephi should be more popular than Cytoscape. It has been mentiond 31 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.

Cytoscape mentions (11)

  • A Canadian payroll dependency chart
    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 / 3 months ago
  • Budō Lineage Tree: a community-driven database and interactive explorer
    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: 10 months ago
  • Any advice on a community detection algorithm?
    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
  • Lost interactive graph (as in nodes + edges) editing tool
    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: over 1 year ago
  • Gephi – The Open Graph Viz Platform
    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 / almost 2 years ago
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Gephi mentions (31)

  • The Hunt for the Missing Data Type
    The following are not exactly what you have asked for. https://gephi.org/ This implements lots of graph visualization algorithms. https://strlen.com/treesheets/ Excel for tree data. - Source: Hacker News / 24 days ago
  • 🇺🇳 Discover a country UN SDGs concerns w/ Open Metadata on Neo4J
    🧑‍🎨 Enjoy some movie data art experience with Gephi and Runway. - Source: dev.to / 5 months ago
  • piece of software to find /crawl information about yourself?
    Maybe try exporting your data from spiderfoot and use a graph tool like Gephi to import your data to and have it generate a graph for you. Source: 12 months ago
  • Countries with the most military conflicts according to Wikipedia (List of wars) [OC]
    Tool: custom python scripts and Gephi. Source: about 1 year ago
  • [OC] I've looked up at +40 000 League Of Legends games to visualize the most common team compositions
    Datasource : https://developer.riotgames.com/apis Tool used : https://gephi.org Network Algorythm : Force Atlas 2. Source: about 1 year ago
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What are some alternatives?

When comparing Cytoscape and Gephi, you can also consider the following products

Graphviz - Graphviz is open source graph visualization software. It has several main graph layout programs.

yEd - yEd is a free desktop application to quickly create, import, edit, and automatically arrange diagrams. It runs on Windows, Mac OS X, and Unix/Linux.

KeyLines - The JavaScript toolkit for graph visualization

UCINET - UCINET for Windows is a software package for the analysis of social network data.

NodeXL - Home

draw.io - Online diagramming application