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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses.

Ben C Stöver1, Kai F Müller

  • 1Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, 48149 Münster, Germany. stoever@bioinfweb.info

BMC Bioinformatics
|January 7, 2010
PubMed
Summary
This summary is machine-generated.

TreeGraph 2 is a new graphical editor for phylogenetic trees that helps researchers combine and visualize data from multiple analyses. This tool facilitates the identification and presentation of incongruences, aiding in the creation of publication-ready figures.

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Area of Science:

  • Phylogenetics
  • Bioinformatics
  • Computational Biology

Background:

  • Phylogenetic analyses increasingly integrate diverse and potentially conflicting data sources.
  • Multiple inference techniques are commonly used, necessitating methods to compare resulting tree topologies.
  • Efficiently comparing and merging statistical support values from different analyses is crucial for robust phylogenetic interpretation.

Purpose of the Study:

  • To develop a user-friendly graphical editor for phylogenetic trees that facilitates data integration and visualization.
  • To provide tools for identifying and graphically representing incongruences between different phylogenetic analyses.
  • To enable the creation of publication-quality phylogenetic figures.

Main Methods:

  • Development of TreeGraph 2, a GUI-based graphical editor for phylogenetic trees.
  • Implementation of automatic data combination from various phylogenetic analyses or dataset subsets.
  • Inclusion of versatile editing and formatting options, including node/branch data import, calculation, filtering, and free formatting.
  • Support for standard tree editing operations and clade manipulation.
  • Output in multiple graphic formats (SVG, PDF, PNG).

Main Results:

  • TreeGraph 2 enables the automatic combination of information from different phylogenetic analyses.
  • The software visually highlights and presents incongruences within the data.
  • Extensive editing and formatting capabilities allow for customized tree visualization, including dynamic assignment of visual properties to node/branch data.
  • Users can import, calculate, filter, and format unlimited variables for nodes and branches.
  • The tool supports manual tree construction and modification, including clade copying and insertion.

Conclusions:

  • TreeGraph 2 is a user-friendly, documented application for producing publication-ready phylogenetic trees.
  • It effectively displays numerous annotations and facilitates their import and combination.
  • The application offers a wide array of editing and formatting operations for enhanced phylogenetic visualization.