| Name | Description | OS | License | Site |
|---|
| BioTapestry | interactive tool for building, visualizing, and simulating genetic regulatory networks | multiplatform (Java-based) | LGPL | http://www.biotapestry.org |
| Cytoscape | data integration, network visualization, and analysis | multiplatform (Java-based) | LGPL | http://www.cytoscape.org/ |
| GenMAPP | visualize and analyze genomic data in the context of pathways | Windows | Apache License | http://www.genmapp.org/ |
| MATLAB | tool for modeling, simulating, and analyzing dynamic biological systems | Windows, Linux, macOS | Proprietary | https://www.mathworks.com/products/simbiology.html |
| MEGA | free, online, open-source, phylogenetic analysis, drawing dendrograms etc. | Windows/DOS-Win/Mac/Linux | Shareware | http://www.megasoftware.net/ |
| PathVisio | tool for displaying and editing biological pathways | multiplatform (Java-based) | Apache License | http://www.pathvisio.org/ |
| InCroMAP | tool for the integration of omics data and joint visualization of experimental data in pathways | multiplatform (Java-based) | LGPL | http://www.cogsys.cs.uni-tuebingen.de/software/InCroMAP/ |
| Pathview | pathway based data integration and visualization, easy to use and integrate into pathway analysis | multiplatform (R/Bioconductor) | GPL | http://pathview.r-forge.r-project.org/ http://bioconductor.org/packages/release/bioc/html/pathview.html |
| SBMLDiagrams[2] | Python API to display and edit SBML layout/render extension | multiplatform | MIT | https://github.com/sys-bio/SBMLDiagrams |
| Systrip | analysis of time-series data in the context of biological networks | Windows, Linux | LGPL, GPL | https://tulip.labri.fr/TulipDrupal/?q=systrip | |
