Recent development of the phylogenetic tree editor TreeGraph 2

Stöver BC, Wiechers S, Müller KF

Abstract

TreeGraph 2 is a user friendly and widely used tree editor with the main focus on processing, visualizing and comparing phylogenetic trees carrying numerous annotations. Since its initial publication a number of features have been added. The ability to import and visualize probabilities for ancestral character states (as reconstructed by software packages like BayesTraits) e.g. by pie charts attached to internal nodes has been added. A special reader allows importing according data from the BayesTraits-specific format, 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. If nodes in one tree are selected, TreeGraph 2 directly visualizes according nodes or regions with conflicting topologies and support in other opened trees. Calculating branch and node annotations from each other using custom expressions has been extended by several new functions which e.g. allow whole columns (one type of annotation from all nodes in a tree) or rows (all annotations on one node) 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. The poster introduces the new features of TreeGraph 2 and shows examples for their application 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/