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The main objective of this project is to provide new models, algorithms and tools to increase significantly the knowledge on the evolution of gene in genomes. More particularly, we aim at disentangling the various events that together constitute the history of genes. In the same time we aim at inferring the relationship between the major groups of living organisms. At short range, we hope to make decisive progress on the early history of the different bacterial groups and on the parental relationship of the early eukaryotes. Global knowledge on gene transfers, duplications and losses events, e.g. average rate in specific lineages, are obtained in the process. Ultimately we aim at unraveling the history of the early branches of life, e.g. relationships between the major groups of bacteria, archaebacteria and first eukaryotes.

Knowledge inferred by methods proposed during the project are in the process to be stored in the project database which is made available through a Web portal (see below).

Some programs we proposed allowed to scale-up computations of the history of gene families according to pre-existing models, while other propose a novel approach optimizing altogether the gene tree topologies, the species tree topology and the evolutionary events such as duplications, losses, transfers and gains in a global inference cycle.

We also propose new visualization tools for exploring both annotations on the data and our gene history inferences.

By putting our software and inferred knowledge freely available (see Resources page), we intend to encourage the study of the evolution of genes and genomes, which have in turn many environmental and medical applications.

A presentation of the work performed in the project is available here

Database of gene histories inferred during the project

An experimental version of the web site allowing to query the inferences is made available at

The database and site should be fully functional by june 2012. Comments are welcomed.


Emerging domains Affaires Européennes
et Internationales
Région Languedoc-Rousillon

Webmaster: Jean-François Dufayard
Former webmaster: Céline Scornavacca