WP4

Posted on octobre 7, 2010 by

Phylogeny and Comparative Genomics

ReNaBi’s platforms are developing algorithms for phylogenetic reconstruction (e.g. PhyML, Guindon et al. 2010) and tools for analyzing and viewing trees (e.g. TreeDyn or NJplot). These works are implemented in software applications that we distribute on the web; they may be downloaded and/or executed on-line. We also design integrated pipelines to compute multiple alignments, build trees and view the results in a user friendly environment (SeaView program, Gouy et al. 2010, and http://www.Phylogeny.fr/ web server, Dereeper et al. 2008). These programs and services are highly cited (PhyML >3,000 since original publication in 2003, SeaView >1,000 since original publication in 1996, cf. Web of Science) and widely used worldwide (Phylogeny.fr 10,000 analyses per month).
We are also working out phylo and comparative genomic databases, which are outstanding resources to elucidate the evolution and function of genes. HOVERGEN, HOGENOM and HOMOLENS (Penel et al. 2009, http://www.prabi.fr/) contain protein gene sequences clustered into groups of homologs. They integrate multiple sequence alignments and phylogenetic trees, and are regularly used for evolutionary studies (> 250 citations). GREENPHYLDB (Rouard et al. 2010) contains plant multigenic families and their associated orthology relationships derived from phylogenetic analyses. SOUTHGREEN provides a large panel of tools to analyze the genomes of tropical agronomy plants. All these databases are widely accessed (SOUTHGREEN 50,000 accesses per month, http://southgreen.cirad.fr/).

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