ColorTree: a batch customization tool for phylogenic trees

In this note, we introduce ColorTree, a simple yet powerful batch customization tool for phylogenic trees. Based on pattern matching rules, ColorTree applies a set of customizations to an input tree file, e.g., coloring labels or branches. The customized trees are saved to an output file, which can then be viewed and further edited by Dendroscope (a freely available tree viewer). ColorTree runs on any Perl installation as a stand-alone command line tool, and its application can thus be easily automated. This way, hundreds of phylogenic trees can be customized for easy visual inspection in a matter of minutes.ColorTree allows efficient and flexible visual customization of large tree sets through the application of a user-supplied configuration file to multiple tree files.Studies in comparative genomics, e.g., analyzing protein family evolution [1-3] or lateral gene transfers [4-7], typically generate large sets of phylogenic trees. Visual inspection of these trees is often necessary, as automated algorithms are not yet sufficiently flexible and reliable [8,9]. The aim of such analyses is often to check for consistency with given null hypotheses (e.g., the clustering of gene copies from known monophyletic groups). This task is often simplified by manual customization of the trees prior to inspection. Customizations usually involve changes of foreground and background colors of specific labels, line-width and color of associated branches, and other aspects of a phylogenic tree. The majority of existing tree viewing programs allow the customization of one or a few opened trees within reasonable time; few also allow to save and re-open customized results [10,11]. However, such manual customization becomes time-consuming and error prone for large trees (the tree of life or the phylogenic tree of NCBI taxonomy, for example) or large tree numbers. In some modern tree-editors published recently, TreeDyn [12] and Dendroscope [13] for example, scripting and command-line consol