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alexis
AGPL 3.0
free
phylogeny,forceatlas
Layouts
1st March 2011
1st March 2011
Gephi 0.7-beta
Linux Mac Windows

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Introduction

A phylogeny oriented 3D force-directed layout.

Plugin Owner's Notes

This plugin has been developped by Alexis Jacomy , within the European research project TINA (FP7-ICT-2009-C - project number 245412). Phylogeny3D works like exactly like a 3D ForceAtlas, but with the nodes sliding on their (xOy) plane, and the distances are computed considering the 3 axes, including even (Oz). The repulsion and attraction coefficients are doubled (one for the horizontal pairs, one for the vertical pairs), but they work exactly like in the ForceAtlas. See: tinasoft.eu/phylo3D

Phylogeny 3D, 4.0 out of 5 based on 1 rating

3 comments feed

  1. 1
    anonymous

    This plugin has vertical and horizontal settings only. That’s two axes, not three. The end product is two-dimensional; This is not a true 3D algorithm and naming it as such is misleading.

  2. 2
    alexis

    Indeed, the plugin description might not be clear enough :

    One common way to visualize phylogenetic graphs is to display each generation of nodes on a line, such as one node and its parents/children are the nearest as possible from each other (like on this picture: http://pandasthumb.org/evolutionvines-thumb-500×417.jpg). Phylogeny 3D works as well, but with parallel layers in a 3D space instead of parallel lines on a plan.

    So, the nodes will slide on their own layer, but the forces are considering the 3D distance between pairs of nodes, contrarily to the other force directed layout algorithms available in Gephi (ForceAtlas, Fruchterman, etc…)

    And so, since the Z value of each node is never modified by Phylogeny 3D, you have to set it by yourself before starting the algorithm. If you don’t, since the default value is 0, all your nodes will be on the same layer, and finally Phylogeny 3D will look exactly like any other 2D force directed layout.

    There is currently no way in Gephi to set the Z values of your nodes from a numerical attribute, but if you can install Netbeans and build/compile Gephi by yourself (instruction are here: http://gephi.org/developers/intro/), I have a fork with a ranking feature that can do this (here is the related fork: https://github.com/jacomyal/gephi).

  3. 3
    Al

    What version of your plugin works with GEPHI 0.7 and/or 0.8

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