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Bioinformatics Vol. 19 no. 7 2003
Pages 851-858
© 2003 Oxford University Press

ALES: cell lineage analysis and mapping of developmental events

V. Braun 1,*, R. B. R. Azevedo 2,3, M. Gumbel 1, P.-M. Agapow 2, A. M. Leroi 2 and H.-P. Meinzer 1

1 Division of Medical and Biological Informatics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D-69120, Germany
2 Department of Biology, Imperial College, Silwood Park, Ascot, Berks SL5 5PY, UK
3 Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA

Received on July 29, 2002 ; revised on December 4, 2002 ; accepted on December 14, 2002

Motivation: Animals build their bodies by altering the fates of cells. The way in which they do so is reflected in the topology of cell lineages and the fates of terminal cells. Cell lineages should, therefore, contain information about the molecular events that determined them. Here we introduce new tools for visualizing, manipulating, and extracting the information contained in cell lineages. Our tools enable us to analyze very large cell lineages, where previously analyses have only been carried out on cell lineages no larger than a few dozen cells.

Results: Ales (A Lineage Evaluation System) allows the display, evaluation and comparison of cell lineages with the aim of identifying molecular and cellular events underlying development. Ales introduces a series of algorithms that locate putative developmental events. The distribution of these predicted events can then be compared to gene expression patterns or other cellular characteristics. In addition, artificial lineages can be generated, or existing lineages modified, according to a range of models, in order to test hypotheses about lineage evolution.

Availability: The program can run on any operating system with a compliant Java 2 environment. Ales is free for academic use and can be downloaded from http://mbi.dkfz-heidelberg.de/mbi/research/cellsim/ales.

Contact: CellO{at}dkfz-heidelberg.de

* To whom correspondence should be addressed.


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