New comparison and annotation methods of the phylogenetic tree editor TreeGraph 2

Wiechers S, Müller KF, Stöver BC

Zusammenfassung

TreeGraph 2 is a user friendly tree editor with the main focus on processing, visualizing and comparing phylogenetic trees carrying numerous annotations. Here, new features added since its initial publication in 2010 are presented. The ability to import and visualize probabilities for ancestral character states (e.g. by pie charts attached to internal nodes) has been extended. A special reader allows importing according data from the software package BayesTraits, while importing from similar software is indirectly possible using the new and more powerful annotation table import function. In addition to the published feature that compares conflicting support values from alternative trees, a new visual comparison method allows the user to directly investigate topological and support differences by highlighting according nodes or regions with conflicting topologies and support in multiple opened trees. Calculating node and branch annotations from each other using custom expressions has been extended by several functions which e.g. allow whole columns or rows as input. Additional new features include the closest possible sorting of terminal nodes according to a specified order, automatic collapsing of internal nodes depending on annotations (e.g. support) or rerooting trees by a given outgroup which may be in topological conflict with the tree. This poster also shows the application of TreeGraph in a recent project investigating the influence of different automated and manual multiple sequence alignments of non-coding sequences containing certain microstructural mutations on phylogenetic inference. Software and poster download and documentation: http://treegraph.bioinfweb.info/