Dereeper A. auteur aut IRD Guignon V. auteur aut IRD Blanc G. auteur aut IRD Audic S. auteur aut IRD Buffet S. auteur aut IRD Chevenet François auteur aut IRD Dufayard J. F. auteur aut IRD Guindon S. auteur aut IRD Lefort V. auteur aut IRD Lescot M. auteur aut IRD Claverie J. M. auteur aut IRD Gascuel O. auteur aut IRD text journalArticle eng text/pdf born digital access Phylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, the phylogenetic reconstruction and the graphical representation of the inferred tree. The Phylogeny.fr platform transparently chains programs to automatically perform these tasks. It is primarily designed for biologists with no experience in phylogeny, but can also meet the needs of specialists; the first ones will find up-to-date tools chained in a phylogeny pipeline to analyze their data in a simple and robust way, while the specialists will be able to easily build and run sophisticated analyses. Phylogeny.fr offers three main modes. The One Click mode targets non-specialists and provides a ready-to-use pipeline chaining programs with recognized accuracy and speed: MUSCLE for multiple alignment, PhyML for tree building, and TreeDyn for tree rendering. All parameters are set up to suit most studies, and users only have to provide their input sequences to obtain a ready-to-print tree. The Advanced mode uses the same pipeline but allows the parameters of each program to be customized by users. The A la Carte mode offers more flexibility and sophistication, as users can build their own pipeline by selecting and setting up the required steps from a large choice of tools to suit their specific needs. Prior to phylogenetic analysis, users can also collect neighbors of a query sequence by running BLAST on general or specialized databases. A guide tree then helps to select neighbor sequences to be used as input for the phylogeny pipeline. Phylogeny.fr is available at: http://www.phylogeny.fr/. specialized 020 36 Suppl S W465-W469 2008 0305-1048 https://www.documentation.ird.fr/hor/fdi:010042723 10.1093/nar/gkn180 0305-1048 [F B010042723] https://www.documentation.ird.fr/hor/fdi:010042723 https://www.documentation.ird.fr/intranet/publi/2008/08/010042723.pdf Accès réservé (Intranet de l'IRD) IRD - Base Horizon / Pleins textes 2008-09-19 2017-08-23 fdi:010042723 fre