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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Conventions
  • M1 = Left Mouse Button
  • M3 = Right Mouse Button (or ctrl-M1)
  • CM = Contextual Menu with M3

    Files suffix:
  • .nwk: newick string
  • .tlf: Treedyn Label File
  • .tds: TreeDyn Script
  • .tgf: Treedyn Graphic File

    • Hands-On
  • Introduction to TreeDyn Updated June 03 2006
  • Annotations and leaf labels
  • HTML exportation

    • Tutorials
  • Basic Operations
  • (Projection - user, newick and annotations)
  • Identification - Querying leaf labels
  • Identification - Locating & Labelling Part I
  • (Identification - Locating & Labelling Part II)
  • Reflection - Multi-trees graphical analysis
  • (Scripting)

    • Interface
  • Annotation Panel
  • Find Panel
  • Identification Panel
  • Library Panel
  • Parameters Panel
  • Preferences Panel
  • Scripting Panel
  • Tree Panel
  • HTML export Panel
    • Packages
  • TreeBASEinterf - TreeBASE interface
  • TreeSPU - supertree
  • TreePAT - tree patterns visualization
  • TreeIG - Interactions Graph
  • TreeXY - Trees & Scatterplot matrices

    • Scripting
  • Examples
  • Commands list
  • TreeDyn Operations
  • TreeDyn Prompt
    • Data
    NWK TGF TLF TDS
    Figure 1
    Figure 2 -
    Figure 3a -
    Figure 3b -
    Figure 4a TreeBASE study ID: S725
    Figure 4b - -
    Figure 4c - -
    Figure 4d - -

    How To ?
  • making an annotations file
  • Leaves*Variables matrix to a TreeDyn labels file
  • target/untarget tree(s)
  • initialize variables
  • opening several trees
  • importing Nexus files
  • Adding Pictures to Canvas
  • Newick strings concatenation
  • Renaming leaves
    • Tips
  • High quality graphics
  • Using Inkscape
  • Postscript visualization
  • PDF export
  • TreeDyn Operations
  • Colors
  • Regular expressions

    • Toolbox