Visualizing a large number of objects defined by a distance matrix or as points in a multidimensional space efficiently has always been challenging.  Three main methods have been developed:  showing the objects as phylogenetic trees in two dimensions, showing the objects as network diagrams, and showing three principal coordinates (or just three arbitrarily chosen parameters from multidimensional coordinates). Here we present a new method which combines the phylogenetic trees with the placement of the objects in three dimensional space.  The new method has been implemented in the ICM suite of programs from MolSoft as an interactive object which is dynamically linked with the underlying data.  The new three dimensional trees are efficient in visualizing complex relationships between large collections of objects of any nature once the distance matrix can be established.  We illustrate this representation on a large collection of chemicals, screening data and biological sequences.

3D phylogenetic trees for visualization and analysis of complex datasets

245th National Meeting (2013)

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