Ben C. Stöver1, Sarah Wiechers1, Kai F. Müller1
1) Evolution and Biodiversity of Plants Group, Institute for Evolution and Biodiversity, WWU Münster, Hüfferstr. 1, 48149 Münster, Germany
Recent development of the phylogenetic tree editor
Citations: Andrew Meade Mark Pagel and Daniel Barker. Bayesian Estimation of Ancestral Character States on Phylogenies. Systematic Biology, 53(5):673-684, 2004.
Ben C. Stöver and Kai F. Müller. TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics, 11(7), 2010.
Poster download: http://www2.ieb.uni-muenster.de/EvolBiodivPlants/en/Publications/ConferenceContribution?id=106662
TreeGraph 2 is distributed under GNU General Public
License Version 3 at the BioInfWeb Software portal:
TreeGraph 2 until 2010
TreeGraph 2 (Stöver & Müller, 2010) is a user friendly and widely used tree editor with
the main focus on processing, visualizing and comparing phylogenetic trees carrying
numerous annotations. Key features are:
Reading trees in Newick, (extended) Nexus format or phyloXML
Importing annotations from table files or combine information from different analyses
Unlimited number of numerical or textual annotations on every branch or node
Exporting trees to various vector and (anti-aliased) pixel graphic formats (e.g. PDF, SVG, EMF or PNG)
Many global and element specific formats like line width or color and text formats and versatile editing and formatting op-
tions, such as automatically setting branch widths or colors according to the value of any attached data column
Editing operations like rerooting, ladderizing or moving and collapsing nodes or copying or manually creating whole clades
Additional new features
Calculating branch and node annotations from each other using custom expressions extended by
several new functions (Fig. 4)
Closest possible sorting of terminal nodes according to a specified order (Fig. 5)
Automatic collapsing of internal nodes depending on annotations (e.g. support) (Fig. 3)
Rerooting by a given outgroup which may be in topological conflict with the tree (Fig. 6)
Current usage in MSA research
The new methods
for tree compari-
son and calculat-
ing branch annota-
tions are currently
used in a project
ed and manual
alignments (of non
Fig. 8 Screenshot of the alignment evaluation software using TreeGraph 2 as a plugin. A
conflict between the two opened trees is visualized by selection synchronizing. Addition-
ally support values generated using other alignment algorithms have been mapped onto
each tree and colored by their difference using the extended feature for calculating anno-
tations from each other.
Visual tree comparison
In addition to the published feature that compares conflicting support
values from alternative trees, a new interactive comparison method al-
lows the user to directly investigate topological and support differences.
Selecting nodes in one tree leads to according selections in other trees.
ly selected in
also found, if
taxa exist in
3b) The ‚
Fig. 7 Interactive comparison of four alternative trees by selection synchronization.
Ancestral character state probabilities
Fig. 2 Two ways of importing ancestral state probabilities and visualize them using pie chart labels.
TreeGraph now allows visualiz-
ing of probability distributions
along branches using pie chart
labels. This is e.g. useful for re-
constructed ancestral character
state probabilities. Such data
can be imported using the
extended table import function.
Additionally, a special reader
for the output of BayesTraits
(Pagel et al., 2004) is available
which saves a lot of time in gen-
erating according figures.
The import table feature can of
course also be used to import
any other type of branch or
node annotations and
TreeGraph offers multiple other
TreeGraph directly imports
BayesTraits output including
probabilities and internal
A tree with resulting
pie chart labels dis-
playing the acenstral
Node/branch data table
containing the imported
data referenced by the
Fig. 3 Example of automatically
collapsing interbal nodes.
Fig. 4 The “Calculate node/
branch data dialog”.
Fig. 5 The “Soft terminal
leaves” dialog. Fig. 6 Rerooting a tree by specifying an outgroup.
2) A node is
the user in
Fig. 1 Example tree from TreeGraph 2