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How to cite us : Zaragüeta-Bagils R., Ung V., Grand A., Vignes-Lebbe R., Cao N., Ducasse J, 2012 LisBeth : New cladistics for phylogenetics and biogeography. C.R Palevol 11(8):563-566.
LisBeth is a standalone computer program that implements the three-item analysis (3ia) for cladistic research in phylogenetics and biogeography. The development of the 3ia approach begun with the works of Gary Nelson, Norman Platnick, Pauline Ladiges (Nelson and Ladiges 1991; Nelson and Platnick 1991; Nelson and Ladiges 1992; Nelson and Ladiges 1996). Recent advances of the method are due to the research by David M. Williams and Malte C. Ebach among others.
Few programs have been developed to implement 3ia:
- A package developed by G. Nelson and P. Ladiges (1992): this package runs on Windows systems only. It converts traditional data matrix into transformed matrix in a format readable by different parsimony analysis software. The package also includes the program TASS (Nelson and Ladiges 1996) that implements paralogy-free subtree analysis for biogeography.
- 3item, a program developed in Java (Ebach, Newman et a. 2003) devoted to biogeography but abandonned.
LisBeth is the only package of computer programs specially designed for three-item analysis (3ia), i.e. phylogenetics and cladistic biogeography. LisBeth graphic user interface (GUI), allows representing hypotheses of homology among taxa or areas directly as rooted trees or as hierarchies, i.e. as nested Venn diagrams. The GUI is used to enter, edit and visualize the hypotheses of homology and the results of their combination using 3ia. It allows a complete description of each character (each tree) and each state (each component of the tree). It may be used for systematics, and it is being adapted for cladistic biogeography.
LisBeth uses an exhaustive or an exact branch-and-bound (default option) method for searching the optimal trees using the principle of compatibility. Because of algorithmic complexity of branch-and-bound, the number of terminal taxa or of endemic areas present in paralogy-free subtrees that may be entered for compatibility search is about 20. Note that because 3ia works with rooted trees, i.e. Cladistic relationships, the upper limit is lower than for parsimony programs.
If a search with a higher number of terminals is needed, LisBeth allows an export into a matrix of characters/taxa in order to run it on any parsimony program. Note however, that in this case, some of the valuable functions that LisBeth implements will not be active, because the results from compatibility analysis are needed. Nevertheless, the most parsimonious trees found by parsimony programs will be correct.
LisBeth outputs the optimal trees into a window of the interface, from where they can be displayed as trees or hierarchies using Venn diagrams. There is always a tree that corresponds to the intersection tree, i.e. to the intersection of all the optimal trees (the intersection tree is not a consensus). If a single optimal tree is found, the intersection tree is identical to it.
LisBeth gives the retention index of each displayed tree, including the intersection tree, and the compatibility index, i.e. the proportion of the tree-item statements deduced from the hypotheses of homology (the coded characters) that are compatible with the tree displayed. For more technical help, please refer to the documentation accessible from the "Help" menu of the GUI.
The LisBeth package includes the following components:
- A set of line-mode tools that run in command-line mode (a DOS box on Windows) or as sub-process launched by any supervisor program. These tools read their input from a data file and produce computed output to the terminal and/or a file. Each tool is dedicated to a specific task; see their documentation for details. Note that the tools that use a lot of computer resources can be run in multi-thread mode in order to take full benefit of multi-processors architecture, if available.
- the main module (3ia) which searches the optimal trees,
- a module (3iaxper) for translation of Xper2 database to LisBeth input file, allowing import of Xper² trees for LisBeth computation. See Xper² web page for more information on Xper²,
- a module (3iahifi) dedicated to the computation of fit index still under development,
- a module (3area) devoted to Biogeography, more precisely, to Area Cladistics,
- a module (3iamatx) that converts a matrix to an input file for LisBeth,
- a module (3iapr), which computes the intersection of optimal trees,
- a module (3iaout) which translates the output of LisBeth into files complying with popular Nexus or Component software.
- A graphic user interface (GUI), providing several high level functionalities. First, it acts as a supervisor above the line-mode tools, hiding the details of file formats, command line syntax and interpretation of results. The program does not compute new data itself. It helps in creating data input files for these tools, as well as in displaying in a convenient way a complex set of results. Only a few of the line-mode tools capabilities are currently superseded by the graphic interface, but this is in our near plans to increase its functionalities. Moreover, the graphic interface can be use as a tool dedicated to the building and displaying population of rooted trees, which we already have experimented to be very useful in pedagogic context. This program was developed mainly in Python language for portability reasons, with small modules in C. See official Python site http://www.python.org to know more about Python.
These programs were developed in C language for efficiency reasons. The current list includes:
All the programs are internationalized. Currently, two languages are available: French and English versions.
This program is free. However, it is not open source. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License. The program is not guaranteed to be bug-free. The authors are not responsible of any data loss or errors resulting from the use of the program.
Please, feel free to contact the authors if you find any surprising result or manifest bug, or if you need any help with the program. Suggestions to improve the program are welcome.
The program should be cited as: Ducasse, J., Cao, N. & Zaragüeta-Bagils, R., 2008: LisBeth. Three-item analysis software package. Laboratoire Informatique et Systématique, UPMC Univ Paris 06, UMR 7207 (CR2P) CNRS MNHN UPMC.
Older versions (formerly known as "Nelson05") are still fully compatible. LisBeth is available on Windows and Linux platforms. Both distributions include the following contents:
- A set of line-mode executable tools and shared libraries. No source available,
- A set of Python interpretable modules (bytecode compiled only), altogether constituting the graphic user interface,
- A set of technical companion files: message catalogs, filters, configuration files,
- A set of detailed documentation describing what each of the tools actually computes. In addition, a beginner’s guide is provided.
LisBeth has been tested on Windows™ 2000 and XP(SP2 and SP3).
The distribution comes as an executable installer. Run the installer and follow the screens sequence. The installer was created with NSIS (Nullsoft) utility: see http://nsis.sourceforge.net.
Download the LisBeth Read-me and installation guide: (available soon, sorry for the inconvenience).
Download the LisBeth installer for Windows.
Note on using the Python graphic interface
The package includes only the lightweight modules of the graphic application. You need an operational Python distribution installed on your computer in order to run the application; version 2.5 or later is needed. If necessary, you can download the Python distribution from its main website (see above).
Alternatively, if you do not want to install the entire Python distribution on your computer (why not?), LisBeth gives you a last chance to appreciate its graphic interface, providing a stand-alone but heavier executable version.
This executable version was created with the py2exe extension of Python.
Download the LisBeth installer for stand-alone graphic interface: download.
LisBeth has been tested on the following platforms:
- Mandrake 9.1,
- Mandriva 10.0.
The distribution comes as a compressed tar file (waiting for a convenient rpm in a near future).
Download the LisBeth Read-me and installation guide: (available soon). Download the LisBeth package for Linux: (available soon).
Note for the usage of the Python graphic interface:
The package includes only the lightweight modules of the graphic application. You need an operational Python distribution installed on your computer in order to run the application; version 2.5 or later is needed. Also, be sure to have the Tcl-Tk package installed. Both are usually included in the Linux distribution, but not necessarily installed. If necessary, you can download the Python distribution from its main website (see above).