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57 changes: 0 additions & 57 deletions compare.html
Original file line number Diff line number Diff line change
Expand Up @@ -118,22 +118,6 @@ <h2>Feature comparison</h2>
<td class="tool"><span class="yes">Yes</span> — interactive GUI</td>
<td class="tool"><span class="yes">Yes</span> — interactive GUI</td>
</tr>
<tr>
<td>Built-in network analysis (centralities, communities, etc.)</td>
<td class="tool"><span class="warn">Descriptive summaries</span> — analysis is done upstream and uploaded as attributes</td>
<td class="tool"><span class="yes">Extensive</span> — multilayer centralities, communities, reducibility</td>
<td class="tool"><span class="warn">Some</span> — degree, betweenness, clustering, community detection</td>
<td class="tool"><span class="yes">Extensive</span> — statistics, modularity, centralities</td>
<td class="tool"><span class="yes">Extensive</span> — via apps (e.g. clusterMaker, NetworkAnalyzer)</td>
</tr>
<tr>
<td>3D rendering</td>
<td class="tool"><span class="warn">Pseudo-3D</span> — oblique stacked-layer projection</td>
<td class="tool"><span class="yes">Yes</span> — 3D (OpenGL)</td>
<td class="tool"><span class="yes">Yes</span> — true 3D scene</td>
<td class="tool"><span class="warn">Mostly 2D</span></td>
<td class="tool"><span class="warn">Mostly 2D</span></td>
</tr>
<tr>
<td>Figure / data export</td>
<td class="tool">PNG, JPG, PDF; reproducible session file (data included)</td>
Expand All @@ -154,47 +138,6 @@ <h2>Feature comparison</h2>
</table>
</div>

<h2>Where each tool is strongest</h2>
<h3>MiRA</h3>
<p>
MiRA is the tool to reach for when you want to <em>see</em> 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 <a href="https://github.com/Ecological-Complexity-Lab/emln">emln</a> R package, and
saves a self-contained session file that reopens the full visualization with its data.
</p>
<h3>muxViz</h3>
<p>
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.
</p>
<h3>Arena3D<sup>web</sup></h3>
<p>
Arena3D<sup>web</sup> 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.
</p>
<h3>Gephi</h3>
<p>
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.
</p>
<h3>Cytoscape</h3>
<p>
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.
</p>

<hr>
<p class="note">
Claims about MiRA are drawn from its source code and manual. Claims about muxViz,
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