- MiRA is the tool to reach for when you want to see a multilayer network quickly and - interactively without installing anything or writing code. It is the only tool in this set - that combines dedicated bipartite layouts with geographic layer placement — the two features - ecological multilayer networks most often need — alongside live filtering, cross-layer - highlighting, and seven linked visualization modes. It reads JSON or CSV, or plots directly - from the emln R package, and - saves a self-contained session file that reopens the full visualization with its data. -
-- muxViz is the most analytically complete tool for multilayer networks. If you need multilayer - centralities, community detection, reducibility analysis, or georeferenced layers and you are - comfortable in R, muxViz is hard to beat. Its interactivity is limited compared with a live - web app, and it does not handle bipartite networks, but its analytical depth is a genuine - strength. -
-- Arena3Dweb renders beautiful, fully interactive true-3D multilayer scenes in the - browser and exposes an API for integration into other pipelines. It was designed for - biomedical networks and does not support bipartite structures or geographic layouts, but for - immersive 3D exploration and programmatic embedding it is excellent. -
-- Gephi is a mature, general-purpose network tool built for large single-layer graphs. Its - layout algorithms, statistics, and ability to handle very large networks are outstanding. It - is not multilayer-native and needs a desktop install, but for scale and general graph - analysis it remains a standard. -
-- Cytoscape is the standard for molecular and biological network analysis, with a large - ecosystem of apps for enrichment, clustering, and data integration. It is a desktop - application built around single-graph analysis rather than multilayer visualisation, but its - app ecosystem and analytical reach are major strengths. -
-Claims about MiRA are drawn from its source code and manual. Claims about muxViz,