TreeDyn: towards dynamic graphics and annotations for analyses of trees

Abstract

Background: Analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as taxonomic descriptions or gene functions that can hardly be encoded within the tree itself (if using popular tree formats). Consequently, a tedious manual analysis and post-processing of the tree graphics are required if one needs to use external information for displaying or investigating trees.

Results: We have developed TreeDyn, a tool using annotations and dynamic graphical methods for editing and analyzing multiple trees. The main features of TreeDyn are 1) the management of multiple windows and multiple trees per window, 2) the export of graphics to several standard file formats with or without HTML encapsulation and a new format called TGF, which enables saving and restoring graphical analysis, 3) the projection of texts or symbols facing leaf labels or linked to nodes, through manual pasting or by using annotation files, 4) the highlight of graphical elements after querying leaf labels (or annotations) or by selection of graphical elements and information extraction, 5) the highlight of targeted trees according to a source tree browsed by the user, 6) powerful scripts for automating repetitive graphical tasks, 7) a command line interpreter enabling the use of TreeDyn through CGI scripts for online building of trees, 8) the inclusion of a library of packages dedicated to specific research fields involving trees.

Conclusion: TreeDyn is a tree visualization and annotation tool which includes tools for tree manipulation and annotation and uses meta-information through dynamic graphical operators or scripting to help analyses and annotations of single trees or tree collections.

Figure 1

Screen shot of a TreeDyn session using Projection functionalities. TreeDyn enables "on the fly" annotation of nodes or leaf labels using the ToolBox (a). The user selects a tool, for instance "Annotate Subtree, symbol", selects a symbol and a color and then annotates tree elements (see corresponding arrows). Bitmaps may be also imported and linked to trees (in this example a pattern visualization of the tree using the TreePAT package of TreeDyn) (b). The "Newick annotation panel" (c) uses the information stored within the newick string such as branch lengths, bootstrap values or taxonomic levels (before or after the ":" character). The Annotation panel (d) enables loading and posting of annotations as graphical elements, facing tree leaves. In this example, a list of binary variables (Sp1, Sp2, etc.) is displayed as a symbol matrix where black and white dots represent the values 1 and 0 respectively in this example.

Figure 2

The Identification operator, localization and labelization. The "Find panel" (a) first allows selection of a highlighting operation: symbol or text annotation but also foreground or background colors, shrinking sub-tree and so on. Then the user either selects a leaf label from a list or enters a string pattern. In this example the pattern "STE*" highlights leaf labels starting with "STE" (red symbol facing leaf labels). Labelization consists in browsing a tree, selecting sub-trees and posting annotations associated to its leaves (b). Localization operates in the opposite direction; it consists in querying annotations associated to leaves and highlighting tree's elements. The Identification panel (c) enables localization and multi-localization (localization on tree collections), it includes a SQL like interpreter. For instance, a "protein tree" is automatically colored according to 'Cellular role' annotations from Yeast Proteome Database [19].

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"...).

Figure 4

Screen shots of TreeDyn packages. Knowing an ID Study (e.g. S725) from TreeBASE, the TreeBASEinterf module (a) allows the fetching of selected tree(s) and their insertion in a TreeDyn document. The TreeIG package (b) allows the drawing of arcs facing the selected leaf labels. Graphical variables of arcs (color, curvation, tabulation) follow a user's definition possibly based on the distances between the leaves. The TreePAT package (c) enables the computation and the coloring of the distance matrix between leaves based on branch lengths. The TreeXY (d) package allows a dynamic linkage between trees and scatterplot matrices.