TreeDyn News 2005

Dec. 23 2005 TreeDyn 187.3 New TreeDyn version (187) and new TreeDynPack (3) (minor bugs solved: TreeDyn alias under Windows, Updating process under OSX...)
TreeDynPack Linux (.tar.gz file)
TreeDynPack MacOSX (.DMG file)
TreeDynPack Windows (.zip file) unzip under "C:\"
Dec. 05 2005

TreeDyn Alert Don't forget to update the treedyn alias properties with the Windows version of TreeDyn. For instance, if you unzip treedynpack under "C:\", edit the properties of "C:\treedynpack\treedyn", then update the "target" entry to "C:\treedynpack\+\treedyn.exe data" and update the "starting" entry to "C:\treedynpack\+"

Dec. 05 2005

TreeDyn Announce: Treedyn Developer As TreeDyn is under the GPL license, any development by a third party is welcome. TreeDyn Developer will offer guidelines on how to add your own packages to TreeDyn.

Nov. 28 2005

TreeDyn Tips Importing TreeDyn graphic in your ".doc" documents. The best way for a high quality TreeDyn graphic in your ".doc" documents is : (1) export the graphic under the Postscript format (2) from the word processor, look at the "Insert" menu, select the "Image from file..." command and select your TreeDyn exported file (".ps"). Then choose the "Encapsulated PostScript" conversion option.

Nov. 27 2005 TreeDyn 186.2 New TreeDyn version (186) and new TreeDynPack (2)
TreeDynPack Linux (.tar.gz file)
TreeDynPack MacOSX (.DMG file)
TreeDynPack Windows (.zip file)
Nov. 17 2005

TreeDyn Announce Treedyn 186.2 (182/183/184/185) soon available for Linux, MacOSX and Windows

Jul. 04 2005

TreeDyn Tips If you are using GSview for Postscript visualisation of the TreeDyn PS export, check on the "EPS Clip" control of the "Options" menu

04.07.2005 TreeDynUpdate number 181 TreeDynPrompt package. This package enables the use of tree graphical operations without this so-complicated TreeDyn graphical interface :)

Comming soon: TreeDynPrompt package, using TreeDyn without graphical interface. the command line : treedyn -tree sample.nwk -label sample.tlf -script sample.tds -out { sample.gif} will returns the graphical traitement on the sample.nwk tree as a Postcript and a GIF file. It uses an annotations file and a script. Would you like to link it to your HTTP server (CGI) ? please don't hesitate to contact me.


TreeDyn application, comming soon: Prodistin Web Site for Functional classification of proteins based on interactions. Posters Sessions:

  • JOBIM 2005 Prodistin Web Site : Un outil disponible sur le Web pour la classification fonctionnelle de protéines à partir de réseaux d'interactions Baudot A., Mouren P., Martin D., Chevenet F., Jacq B., et Brun C.
  • ECCB 2005 WebDistin: a Web tool for the functional classification of proteins from interaction networks Anaïs Baudot, Pierre Mouren, David Martin, François Chevenet, Alain Guénoche, Bernard Jacq and Christine Brun.

TreeDyn Announce. Mac OSX TreeDyn version is under construction. I try to make it available for the JOBIM 2005 Workshop.


TreeDynUpdate number 179 & 180 "Scripting Day" :) The scripting package of TreeDyn has been revised and extended. The corresponding section of the user's manual has been updated also. Scripting Manual. Try it by fetching the 2 followings files and start a TreeDyn session. First load the tree (*.nwk), then the script (*.tds). Tree file: sample01.nwk Script files: sample01.tds

  • The script (with comments)
  • The tree before the script
  • The tree after the script
  • 15.04.2005 TreeDynUpdate number 178 HTML export updated, Display bootstrap values by treshold
    12.04.2005 TreeDynUpdate number 177 SuperTree package updated, new TreeDyn family function: Construction, tools for the building on the fly of tree (Copy&Insertion of sub-tree as new node, as polytomy, Copy&Replace...)
    06.04.2005 Release of
    TreeDynDirect, the TreeDyn "hotline". Don't hesitate to add the email to your contact list if your are using MSN messenger. English & Français spoken.
    29.03.2005 TreeDynUpdate number 176 SuperTree package updated
    16.03.2005 TreeDynUpdate number 175
    Now I will add comments about what's new with TreeDyn versions.
    The 173-175 are related to a very specific package for SuperTree management.
    Nota Bene: the latest version always include all the previous ones.
    13.03.2005 TreeDynUpdate number 174
    11.03.2005 TreeDynUpdate number 173
    08.03.2005 TreeDynUpdate number 172
    23.02.2005 TreeDyn Hands-On, TreeDyn HTML exportation
    Having an online suplementary material for your trees publications ?
    Big trees, Colors, Annotations and URLs linked to trees with the TreeDyn HTML exportation
    18.02.2005 The TreeSub project
    Action Interdisciplinaire Incitative Régionale 2005-2007
    18.02.2005 TreeDynUpdate patch available number 171
    Nota Bene: now there is a version number you can check on the main TreeDyn Panel
    07.02.2005 TreeDyn Hands-On, by R. Christen
  • Introduction to TreeDyn
  • How to use annotation files to label treeleaves
  • 27.01.2005 TreeDyn applications
  • A scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network
    Anaïs Baudot, Bernard Jacq and Christine Brun
    Genome Biology 2004, 5:R6 OpenAccess | PDF
  • Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network
    Christine Brun, François Chevenet, David Martin, Jérôme Wojcik, Alain Guénoche and Bernard Jacq1
    Genome Biology 2003, 5:R6 OpenAccess | PDF
  • 26.01.2005 Building TreeDyn annotations files from Gene Ontology using GOToolBox
    GOToolBox: functional analysis of gene datasets based on Gene Ontology
    David Martin , Christine Brun , Elisabeth Remy , Pierre Mouren , Denis Thieffry and Bernard Jacq
    Genome Biology 2004, 5:R101 OpenAccess | PDF | GOToolBox
  • TreeDyn GuestBook (see Community)
  • TreeDyn chat MSN:
  • TreeDyn chat ICQ: 204 747 943
  • 21.01.2005TreeDyn patch available (TreeDynUpdate)
  • TreeDynPack first release, Windows & Linux (IX-86) OS
  • TreeDynUpdate first release
  • User's Manual, a beginning
  • TreeDyn under GPL License