TreeDyn: towards dynamic graphics & annotations for trees analyses
PRG inter-EPST Bio-informatique CNRS, INSERM, INRA, INRIA, Ministère de la Recherche, 2001-2003, 2002-2004
ACI IMPbio Mathématique et Physique en Biologie Moléculaire, 2004-2006
http://www.treedyn.org

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Why TreeDyn ?

Many powerful tree editors are now available, but existing tree visualisation tools make little use of meta-information related to the entities under study such as taxonomic descriptions, geographic distribution or gene functions. This meta-information is useful for the analyses of trees and their publications, but can hardly be encoded within the tree itself (the so-called newick format).

Consequently, a tedious manual analysis and post-processing of the tree's images is required. Particularly with large trees, multiple trees and multiple meta-information variables.

TreeDyn offers to link unique leaf labels to lists of variables/values pairs of annotations (meta-information), independently of the tree topologies, remaining fully compatible with the basic newick format. These relationships are used by dynamic graphics operators, information visualization methods like Projection, Localization, Labelization, Reflection allowing an interaction from annotations to trees, from trees to annotations and from trees to trees through annotations.

TreeDyn features
  • TreeDyn Overview Version May 2006, pdf file, (~9Mo)
  • is a graphical editor for binary trees
  • manages multi-windows and multi-trees per Window
  • manages meta-information related to the entities under study
  • exporting graphics to several standard file formats (PS, JPG, GIF, PNG...)
  • exporting graphics with HTML encapsulation
  • saving/restoring graphical analysis (TGF format)
  • is scriptable
  • multi-platforms: MacOSX (Tiger), Linux & Windows Operating Systems
  • is freeware
  • is Open Source (GPL, see below)
  • is always under active development

  • TreeDyn Screenshots

    Package TreeXY

    Package TreeIG

    Package TreeBASEinterf

    Package TreePAT

    Multi-tree graphical analysis

    Identification
    Protein function prediction
    (Brun et al., 2003, Genome Biology)

    Annotation

    Annotation

    Phylogeography

    Annotation, Black&White, binary variables patterns

    HTML exportation, online "Suplementary material" for publication

    SuperTree Analyses