ScripTree

ScripTree: scripting phylogenetic graphics

Summary: There is a large amount of tools for interactive display of phylogenetic trees. However, there is a shortage of tools for the automation of tree rendering. Scripting phylogenetic graphics would enable the saving of graphical analyses involving numerous and complex tree handling operations and would allow the automation of repetitive tasks. ScripTree is a tool intended to fill this gap. It is an interpreter to be used in batch mode. Phylogenetic graphics instructions are stored in a text file and performed in a sequential way. Such instructions are related to tree rendering as well as tree annotation. ScriptTree is written in Tcl/Tk making it a cross-platform application, e.g. suitable for Windows and Unix-like systems, including OS X. It can be used either as a standalone package or included in a bioinformatic pipeline and linked to a HTTP server. See the "Examples" section for a ScripTree demonstration by using a web interface. See the "Download & Install" section for downloading ScripTree and its user's manual.

Project

Financial support

This project is supported by grants from:

IRD-SPIRALES 2007-2008
"ScripTree: a scripting language for phylogenetic tree graphics"
Francois Chevenet (lead) & Richard Christen

ANR Domaines Emergents 2009-2011
"PhylAriane: Phylogenomique - Algorithmes et Representations Intégrés pour l'ANalyse de l'Evolution du vivant"
Berry et al. 2008.

Contact

chevenet@ird.fr
IRD-GEMIbiv

chevenet@lirmm.fr
LIRMM-MAB

Citation

ScripTree: scripting phylogenetic graphics
François Chevenet, Olivier Croce, Maxime Hebrard, Richard Christen and Vincent Berry
Bioinformatics 2010 26(8):1125-1126

www.scriptree.org

Examples

Open the example tabs below and clic the "load" button. Then clic the "Submit" button. You can also Copy/Paste your own data (newick string(s), script and annotations).

Example 1: tree, l_symbol_annotation, l_bracket_annotation, query_newick, query_annotation

Example 2: tree, l_bracket_annotation, l_arc_annotation

Example 3: tree, hi, query_annotation

Example 4: tree, hi, l_chart_annotation, s_shape_annotation, l_string_annotation

Example 5: tree, l_symbol_annotation, query_annotation

Example 6: tree, l_symbol_annotation

Download & Install

ScripTree binaries

Please, note that the next ScripTree release will integrate a new format for annotations. This new format will be CSV. Next ScripTree versions will not be compatible with the current format of annotations

Release 17. The following ScripTree distribution integrates the ScripTree program with example data files (tree, script and annotations, see the "ste" folder). Nothing to install (the Tcl/Tk interpreter is included). It can be used either as a stand-alone package or linked to a HTTP/CGI toolbox (see the "readme.txt" file for more details)

Linux scriptree.tar.gz v.17

OSX scriptreeosx.zip v.17

Windows scriptree.zip v.17

ScripTree tutorials

ScripTree Tutorial #01

ScripTree source

ScripTree is under the GPL license. Copyright © 2008 Chevenet F. chevenet@ird.fr/chevenet@lirmm.fr This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ScripTree source code is here

ScriptTree is written in Tcl/Tk making it a cross- platform application, e.g. suitable for Windows and Unix-like systems, including OS X. It can be used either as a standalone package or included in a bioinformatic pipeline and linked to a HTTP server.

ScripTree manual

ScripTree Manual (html)