 TreeDyn ?
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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.
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 TreeDyn features
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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
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 Projects
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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
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 Thanks
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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
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 Research using TreeDyn
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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
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 www.treedyn.org
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TreeDyn Mailing List:
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TreeDyn is under GPL
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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
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News
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May 2007: TreeDyn 198
May 2007: genbank2treedyn by R. Christen
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Production of TreeDyn annotations files from FASTA, GenBank & ACNUC sequences files
Tutorial
Download
NB: TreeDyn 198.3 is necessary
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May 2007 TreeDyn & www.phylogeny.fr
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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.
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2006
2005
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Update TreeDyn 198.3 (May 2007)
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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...
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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).
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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
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 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
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Screenshots
TreeDyn Citation
Manual