GEMI Bioinformatics F. Chevenet
U.M.R. 2724 CNRS-IRD & U.R. 165 IRD Génétique et Evolution des Maladies Infectieuses
Centre de Recherche I.R.D. 911, Avenue Agropolis - BP 64501 34394 Montpellier Cedex 5 - France

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 links 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, May 2006, pdf, (~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, ...)
  • exporting graphics with HTML encapsulation
  • saving/restoring graphical analysis (TGF format)
  • is scriptable
  • multi-platforms: MacOSX (Tiger), Linux & Windows
  • is freeware
  • is Open Source (GPL, see below)
  • is always under active development

  • Screenshots


    Projects
  • 2007 SPIRALES - IRD, F. Chevenet
  • 2005-2007 Bio-STIC-LR, F. Chevenet
  • 2004-2006 ACI IMPbio, E. Douzery.
  • 2002-2004 inter-EPST Bio-informatique, C. Pasquier
  • 2001-2003 inter-EPST Bio-informatique, F. Chevenet
  • Thanks

    Bañuls Anne-Laure, Barnabé Christian, Bénézé Olivier, Berry Vincent, Biron David, Boriello Caroline, Boudot Anais, Brun Christine, Cance Jerome, Chapon Virginie, Choisy Marc, Christen Richard, Corne Philippe, Douzery Emmanuel, Dujardin Jean-Pierre, Fargette Denis, Fauquet Claude, Godreuil Sylvain, Gouy Manolo, Guénoche Alain, Guez Alex, Hide Mallorie, Jacq Bernard, Leclerc Marie-Claude, Lopez-Ferber Miguel, Meeus Thierry, Oury Bruno, Pasquier Claude, Szmaragd Camille, Tauzin Marc, Tazi Loubna, Vermat Thierry, Vigouroux Yves, Zolli David

    Research using TreeDyn
  • Veron A et al MBE ; 2007 24(3):670-678
  • Piegu B et al Genome Res ; 2006 16: 1262 - 1269
  • Eichler S et al Appl Environ Microbiol ; 2006;72(3):1858-72
  • Zhong W et al Science 2006 ; 311(5766):1481 - 4
  • Baudot A et al Bioinformatics ; 2006; 22(2):248-50
  • Duchene AM et al PNAS 2005 ; 102(45):16484-9
  • Brun C et al Genome Biol ; 2003; 5(1):R6
  • www.treedyn.org
    Locations of visitors to this         page TreeDyn Mailing List:
    TreeDyn is under GPL
    This software is OSI Certified Open Source Software. OSI Certified is a certification mark of the Open Source Initiative TreeDyn source code is ~/treedynpack/+/data
    News
  • May 2007: TreeDyn 198
  • May 2007: genbank2treedyn by R. Christen
    Production of TreeDyn annotations files from FASTA, GenBank & ACNUC sequences files Tutorial Download
    NB: TreeDyn 198.3 is necessary
  • May 2007 TreeDyn & www.phylogeny.fr
    Phylogeny.fr is a free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences. Phylogeny.fr runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences.
  • 2006
  • 2005
  • Update TreeDyn 198.3 (May 2007)
  • Newick annotation panel updated
  • New symbol system
  • New shrink tools
  • Preferences panel
  • Leaf labels extraction tool (file, clipboard)
  • Illustration system updated
  • HTML export updated (multi-trees)
  • RGB matrix annotation
  • HCI updated
  • Read more...

    Update TreeDyn to patch 198 by using the "TreeDyn Update" option from the "Help menu". The latest version always include all the previous ones. If the patching process is stopped while downloading, please reload/install the treedynpack (this bug is now fixed).

    Download TreeDynPack (198.3)
    Linux (.tar.gz file)
    unzip/untar treedynpack.tar.gz. Go to the treedynpack folder and then use the command "./treedyn". You may have to "chmod" treedynpack
    MacOSX (.DMG file)
    after decompression of the DMG file, double-clic on the TreeDyn icon. Copy the disk image file to your application folder or your Home directory
    Windows (.zip file)
    unzip under "C:\". if you have unzip treedynpack.zip under C:\ double click on the treedyn alias. If the treedynpack.zip has been unzip elsewhere, update the treedyn alias properties. For instance, if you unzip treedynpack under "C:\tree", edit the properties of "C:\tree\treedynpack\treedyn.lnk", then update the "target" entry to "C:\tree\treedynpack\+\treedyn.exe data" and update the "starting" entry to "C:\tree\treedynpack\+". Also, you can update the alias icon using the file ~\treedynpack\+\+\icon\itd.ico file
    TreeDyn Citation

    Chevenet F., Brun C., Banuls A.L., Jacq B. and R. Christen TreeDyn: towards dynamic graphics and annotations for analyses of trees BMC Bioinformatics 2006, 7:439

    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 - -
    Manual
    Tutorials Hands-On FAQ Tips