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

Abstract

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/ http://www2.ieb.uni-muenster.de/EvolBiodivPlants/en/Publications/ConferenceContribution?id=107034

Full text

Sarah Wiechers1, Kai F. Müller1, Ben C. Stöver1
1) Evolution and Biodiversity of Plants Group, Institute for Evolution and Biodiversity, WWU Münster, Hüfferstr. 1, 48149 Münster, Germany
New comparison and annotation methods of the
phylogenetic tree editor TreeGraph 2
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.
http://www2.ieb.uni-muenster.de/EvolBiodivPlants
Poster download: http://www2.ieb.uni-muenster.de/EvolBiodivPlants/en/Publications/ConferenceContribution?id=107034
Availability
TreeGraph 2 is distributed under GNU General Public
License Version 3 at the BioInfWeb Software portal:
http://treegraph.bioinfweb.info/
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 combining 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, text formats and versatile editing and formatting options,
such as automatically setting branch widths or colors according to the value of any attached data column
 Editing operations like rerooting, ladderizing, 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
(e.g. functions with whole columns or rows as parameters) (Fig. 3)
 Closest possible sorting of terminal nodes according to a specified
order from a text file or another tree (Fig. 4)
 Automatic collapsing of internal nodes depending
on annotations (e.g. support) (Fig. 5)
 Rerooting by a given outgroup which may be in
topological conflict with the tree (Fig. 6)
Usage in MSA research
The new methods for tree comparison and calculating branch annota-
tions are currently used in a project investigating the influence of
different automated and manual multiple sequence alignments (of non-
coding sequences containing certain microstructural mutations) on
phylogenetic inference.
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 synchroniz-
ing. Additionally support values generated using other alignment algorithms have
been mapped onto each tree and colored by their difference using the extended fea-
ture for calculating annotations from each other.
Ancestral character state probabilities
TreeGraph 2 now allows visual-
izing 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 com-
mand generator for the ances-
tral state reconstruction soft-
ware BayesTraits (Pagel et al.,
2004) and a reader for its out-
put files is available. This saves
a lot of time in running analyses
and generating according
figures.
The import table feature can of
course also be used to import
any other type of branch or
node annotations and
TreeGraph 2 offers multiple
other visualizing options.
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.
3a) The
according
node is
automatical-
ly selected in
this tree.
3c) According
nodes are
also found, if
additional
taxa exist in
a tree.
3b) The
highest
conflicting
support is
selected in
this tree.
Fig. 7 Interactive comparison of four alternative trees by selection synchronization.
1) Selection
synchronizing
is switched
on.
2) A node is
selected by
the user in
one tree.
Fig. 6 Rerooting a tree by specifying an outgroup.
Fig. 5 Example of automatically
collapsing internal nodes.
Fig. 4 The “Sort terminal
leaves” dialog.
Fig. 3 The “Calculate node/
branch data dialog”.
Fig. 1 Example tree from TreeGraph 2
Fig. 2 Two ways of importing ancestral state probabilities and visualizing them using pie chart labels.
TreeGraph 2 directly imports
BayesTraits output including
probabilities and internal
node definitions
A tree with resulting
pie chart labels
displaying the ancestral
state probabilities
Node/branch
data table
containing the
imported data
referenced by
the labels
Table
generated
from other
reconstruc-
tion software
Assign imported
columns to
node/branch
data columns
Automatically
generate com-
mands for a
BayesTraits
analysis
BayesTraits
output