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      TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses

      product-review

      1 , 2 , , 1

      BMC Bioinformatics

      BioMed Central

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          Abstract

          Background

          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.

          Results

          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.

          Conclusion

          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.

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          Most cited references 13

          • Record: found
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          MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment.

           S. KUMAR (2004)
          With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.
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            • Record: found
            • Abstract: not found
            • Article: not found

            TreeView: an application to display phylogenetic trees on personal computers.

             Roderic Page (1996)
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              • Record: found
              • Abstract: found
              • Article: not found

              ATV: display and manipulation of annotated phylogenetic trees.

               C. M. Zmasek,  S. Eddy (2001)
              A Tree Viewer (ATV) is a Java tool for the display and manipulation of annotated phylogenetic trees. It can be utilized both as a standalone application and as an applet in a web browser.
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                Author and article information

                Journal
                BMC Bioinformatics
                BMC Bioinformatics
                BioMed Central
                1471-2105
                2010
                5 January 2010
                : 11
                : 7
                Affiliations
                [1 ]Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, 48149 Münster, Germany
                [2 ]Nees Institute, University of Bonn, Meckenheimer Allee 170, 53115 Bonn, Germany
                Article
                1471-2105-11-7
                10.1186/1471-2105-11-7
                2806359
                20051126
                Copyright ©2010 Stöver and Müller; licensee BioMed Central Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Categories
                Software

                Bioinformatics & Computational biology

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