A visualization of RNA virus phylogenies in the tree shape kernel space (, ) using t-distributed stochastic neighbor embedding (t-SNE).

Abstract

<p>The t-SNE algorithm attempts to find the optimal map of high-dimensional data into a low-dimensional space while preserving the distances among points as much as possible. Thus, the distance between pair of viruses or virus clades (labelled by the same abbreviations as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078122#pone-0078122-g004" target="_blank">Figure 4</a>) is approximately proportional to their mean kernel distance. Groups of virus clades of particular interest are highlighted with the corresponding colours: HIV, red; HCV, yellow; Dengue (DEN), green; IAV-H3, IAV-H1, and IBV (blue).</p