Project

TreeGraph 2 - A feature-rich phylogenetic tree editor

Goal: This project keeps you up to date on the further development of TreeGraph 2, new releases and features.

TreeGraph 2 is an easy to use editor for phylogenetic trees that offers a variety of editing and formatting options. You can interactively compare and combine trees from different (conflicting) analyses and attach an unlimited number of numerical or textual annotations to every node and branch. Newick, Nexus, NeXML, PhyloXML, tables and MrBayes data are supported for I/O.

A complete documentation and tutorials are available here: http://treegraph.bioinfweb.info/Help. If you have further questions, don't hesitate to ask one in this project.

http://treegraph.bioinfweb.info/
https://github.com/bioinfweb/TreeGraph2
http://twitter.com/bioinfweb
Legal notice: http://treegraph.bioinfweb.info/About
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Project log

Ben C Stöver
added an update
Finally, a new version of our phylogenetic tree editor TreeGraph 2 is available.
It contains bug fixes for adding support values from other trees and for compatibility with newer Java versions and many other additions.
 
Michael Herdman
  • 30.81
  • Institut Pasteur International Network
I have been using TreeGraph2 without problem for several years. Recently, however, I get two errors:
'You seem to using TreeGraph 2 for the first time on this system.'
and when opening files I am often asked to send error report with message: 'The error "java.lang.NoClassDefFoundError: org/w3c/dom/ls/DOMInput" occurred.'
This is on openSUSE Linux, with the jarfile in /opt.
 
  • Modified
Rudy J Richardson
  • 93.23
  • University of Michigan
Ben C Stöver : I have nexus files for dendrograms that were generated in a different program (PAST). I would like to use TreeGraph2 to produce the dendrogram plots. The nexus files do not have any color information. I would like to color the terminal node labels (taxa) according to a factor or grouping variable, e.g., -1 = blue, 0 = black, +1 = red (please see the example file attached). How would I go about doing this in TreeView2? I am very new to the use of TreeView2. Thanks.
 
png
tree_example.png
Ben C Stöver
added a research item
Phylogenetics, phylogenomics and related fields have become data-intensive due to increasingly cheaper high-throughput sequencing technologies, the digitization of large biological collections or data contributions from citizen science. An increasing number of computationally accessible methods for analyses that produce derived data, like phylogenetic trees, further contribute to the production of large quantities of potentially reusable data. This opens up new opportunities for data-intense studies, but also creates new challenges for cyberinfrastructure and method development such as meaningful and ideally machine-interpretable annotation of published data to allow easy reuse and automated large-scale data collection.Here we present new functionality of our phylogenetic tree editor, TreeGraph 2, to store, edit and visualize any type of metadata attached to phylogenetic trees or their nodes and branches. TreeGraph 2 has become widely used since its first release in 2008 and offers versatile editing and formatting features in a user-friendly graphical user interface. It now supports the metadata model of NeXML that is based on the Resource Description Framework (RDF) and allows unambiguously describing the relation of metadata to phylogenetic data. The new functionality simplifies necessary metadata annotation of phylogenetic trees to allow their optimal reuse, to document the workflow used to infer them, and to link respective raw data.A similar extension of the metadata model of our multiple sequence alignment editor PhyDE is currently underway. In combination, PhyDE and TreeGraph 2 provide necessary annotation functionality for all major datatypes of phylogenetics. The new functionality is based on our software libraries JPhyloIO and LibrAlign that exhibit their functionality to third-party applications.
Ben C Stöver
added an update
We switched to MantisBT as our bug tracking system, which is now open to all users. Check out http://treegraph.bioinfweb.info/Bugs if you want to report a bug a share a feature request with us.
 
Ben C Stöver
added an update
The TreeGraph 2 source code repository now has a synchronized mirror on GitHub.
Feedback and pull requests are welcome.
 
Ben C Stöver
added an update
We are currently working on extending the metadata model of TreeGraph 2. In addition to the simple string keys (column IDs) currently used to attach metadata to tree nodes or branches, future versions will be able to use RDF-predicates from externally defined ontologies to attach metadata. The aim is to increase accessibility and reusability of phylogenetic metadata processed with TreeGraph 2.
The new metadata model will be fully compatible with that of NeXML. NeXML will therefore replace TreeGraph's native XTG format in the future to increase interoperability.
Further information:
 
Ben C Stöver
added 5 research items
Today it is common to apply multiple potentially conflicting data sources to a given phylogenetic problem. At the same time, several different inference techniques are routinely employed instead of relying on just one. In view of both trends it is becoming increasingly important to be able to efficiently compare different sets of statistical values supporting (or conflicting with) the nodes of a given tree topology, and merging this into a meaningful representation. A tree editor supporting this should also allow for flexible editing operations and be able to produce ready-to-publish figures. We developed TreeGraph 2, a GUI-based graphical editor for phylogenetic trees (available from http://treegraph.bioinfweb.info). It allows automatically combining information from different phylogenetic analyses of a given dataset (or from different subsets of the dataset), and helps to identify and graphically present incongruences. The program features versatile editing and formatting options, such as automatically setting line widths or colors according to the value of any of the unlimited number of variables that can be assigned to each node or branch. These node/branch data can be imported from spread sheets or other trees, be calculated from each other by specified mathematical expressions, filtered, copied from and to other internal variables, be kept invisible or set visible and then be freely formatted (individually or across the whole tree). Beyond typical editing operations such as tree rerooting and ladderizing or moving and collapsing of nodes, whole clades can be copied from other files and be inserted (along with all node/branch data and legends), but can also be manually added and, thus, whole trees can quickly be manually constructed de novo. TreeGraph 2 outputs various graphic formats such as SVG, PDF, or PNG, useful for tree figures in both publications and presentations. TreeGraph 2 is a user-friendly, fully documented application to produce ready-to-publish trees. It can display any number of annotations in several ways, and permits easily importing and combining them. Additionally, a great number of editing- and formatting-operations is available.
http://www2.ieb.uni-muenster.de/EvolBiodivPlants/en/Publications/ConferenceContribution?id=94531
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
Ben C Stöver
added a project goal
This project keeps you up to date on the further development of TreeGraph 2, new releases and features.
TreeGraph 2 is an easy to use editor for phylogenetic trees that offers a variety of editing and formatting options. You can interactively compare and combine trees from different (conflicting) analyses and attach an unlimited number of numerical or textual annotations to every node and branch. Newick, Nexus, NeXML, PhyloXML, tables and MrBayes data are supported for I/O.
A complete documentation and tutorials are available here: http://treegraph.bioinfweb.info/Help. If you have further questions, don't hesitate to ask one in this project.