Figure 3.

The Reflection operator for tree collection analyses. Screenshot illustrating reflection used in the study of 27 gene trees from 19 virus species of the Baculoviridae family [38]. Reflection enables the browsing of a source tree and results in highlighting targeted trees. In example (a) the Reflection tool using a strict identity of leaf labels between trees is activated. It enables the selection of the sub-tree {Ld, Bm, Rou, AcM, OpM, Eppo, Se, Maco-A and Maco-B} and allows its highlighting (grey sub-tree background) and every potentially sub-trees of others tree of the collection. Any tree of the collection may be used as a source tree and different highlighting operations are available. Here a symbol insertion facing "HaS" and "HzS" leaf labels and the update of the background for the outgroup"Cuni". In example (b), The Reflection tool using different leaf label sets is activated. The reflection operates from a consensus tree (tree with a grey background) using species names as leaf labels towards a set of trees using genes names as leaf labels. The corresponding annotations file integrates records putting in regards species labels from the consensus tree to genes labels from the others trees (e.g. "ADO reflection {Ado001 Ado002 Ado003 ...}"). With such an annotations file, the reflection operates from the consensus tree (the source tree) to the other trees, and results in highlighting sub-trees background, shrinking and line aspect modifications. For a reflection between genes trees, the annotation file may integrate records linking leaf labels from different trees, as described in the text (for example "Ado001 reflection ADO", "Ado002 reflection ADO"...).