TreeGraph 2

TreeGraph 2 is a Java-based, cross-platform desktop editor for phylogenetic trees, developed by Ben C. Stover and Kai F. Muller at the University of Munster and maintained by the bioinfweb group. It was introduced in a 2010 BMC Bioinformatics paper and remains actively developed under the GNU GPL v3. Its distinguishing focus is not merely drawing a tree but producing publication-quality tree figures that carry rich, per-node and per-branch annotation, and interactively comparing and combining the results of several independent phylogenetic analyses of the same taxa.

The internal data model treats each node and branch as a carrier of an unlimited number of named variables, which may be numeric or textual and either shown or kept invisible. These node/branch data can be imported from spreadsheets or other trees, computed from one another via user-defined mathematical expressions, filtered, and copied between variables. Formatting is data-driven: line width, color, or label style can be set automatically from the value of any chosen variable, so support values, posterior probabilities, or arbitrary metadata drive the visual appearance. A characteristic feature is automated support mapping, which for congruent branches groups equivalent support values under shared label IDs and, for conflicting topologies, flags the maximum contradictory support with user-chosen brackets, asterisks, or colors.

For interchange, TreeGraph 2 imports the common tree serializations, reading format:newick, format:nexus (including hot-comment annotations from tools such as BEAST and MrBayes), format:nexml, and format:phyloxml, plus tabular data and BayesTraits output. Its native on-disk format is XTG (format:xtg), an XML document that preserves the full annotation and formatting state that plainer tree formats cannot represent. Trees are exported as vector or raster graphics, including PDF, SVG, EMF, and PNG, for figures in papers and talks. Later versions delegate parsing and writing to the sibling JPhyloIO library.

Within the broader graph-data and conversion landscape it is a specialized, domain-specific counterpart to general phylogeny tools such as tool:ete, tool:biopython, and tool:phylogeny-fr, and to format-level converters like tool:newick-to-graphml. Its main limitation is scale: it is optimized for careful editing of moderately sized annotated trees rather than for viewing datasets with thousands of taxa, and it is a GUI application rather than a scriptable library, so batch or programmatic pipelines are better served elsewhere.