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BioCodeKb - Bioinformatics Knowledgebase

A graphical editor for phylogenetic trees which allows us to apply lots of graphical formats to the elements of our tree. Moreover, TreeGraph supports several (visible or invisible) annotations (e.g. support values) for every branch or node. These annotations can be imported from Nexus tree files or text files containing data in a table (e.g. exported from a spreadsheet program). TreeGraph is licensed under  General Public License.

A key feature is the interactive comparison and combination of alternative topologies from different analyses. This should also allow for flexible editing operations and be able to produce ready-to-publish figures. A tool, TreeGraph , has developed , a GUI-based graphical editor for phylogenetic. 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. 

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, but can also be manually added and, thus, whole trees can quickly be manually constructed de novo. TreeGraph outputs various graphic formats such as SVG, PDF, or PNG, useful for tree figures in both publications and presentations. TreeGraph 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.

Reducing the total time of the tool changing process by the automatic tool changer system can be also achieved through minimizing the number of movements needed for the actual exchange of the tool, from the tool magazine to the machine spindle.


  • Filtering by bootstrap support values associated with the monophyletic clades

  • Filtering by tree complexity Filtering by family complexity (number of genes per taxon in a tree)

  • Clustering trees (genes) into tree clusters (gene families)

  • Using a reference tree to taxonomically group (tree-format)

  • Read trees in Newick, Nexus format (including annotations in hot comments), NeXML or PhyloXML

  • Import annotations from text files or combine information from different phylogenetic analyses

  • An unlimited number of numerical or textual annotations on every branch

  • Export 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

  • Versatile editing and formatting options, such as automatically setting branch widths or colors according to the value of any attached data

  • Editing operations like rerooting, ladderizing or moving and collapsing nodes or copying or manually creating whole clades

  • Generate commands and import data for ancestral state reconstruction.


Need to learn more about TreeGraph and much more?

To learn Bioinformatics, analysis, tools, biological databases, Computational Biology, Bioinformatics Programming in Python & R through interactive video courses and tutorials, Join BioCode.

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