Phylogeny.fr: robust phylogenetic analysis for the non-specialist Export

@article{Dereeper2008, abstract = {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/ 10.1093/nar/gkn180}, address = {Information G\'{e}nomique et Structurale (IGS), CNRS-UPR2589, IFR-88, Marseille, M\'{e}thodes et Algorithmes pour la Bioinformatique (MAB), LIRMM, CNRS – Univ. Montpellier II and G\'{e}n\'{e}tique et Evolution des Maladies Infectieuses (GEMI), CNRS – IRD, Montpellier, France.}, author = {Dereeper, A. and Guignon, V. and Blanc, G. and Audic, S. and Buffet, S. and Chevenet, F. and Dufayard, J. F. and Guindon, S. and Lefort, V. and Lescot, M. and Claverie, J. M. and Gascuel, O.}, citeulike-article-id = {2803275}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkn180}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/content/36/suppl_2/W465.abstract}, citeulike-linkout-2 = {http://nar.oxfordjournals.org/content/36/suppl_2/W465.full.pdf}, citeulike-linkout-3 = {http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_2/W465}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/18424797}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=18424797}, day = {1}, doi = {10.1093/nar/gkn180}, issn = {1362-4962}, journal = {Nucl. Acids Res.}, keywords = {analyses, bioinformatics, method, phylogenetic, phylogeny, phyml}, month = {July}, number = {suppl\_2}, pages = {W465--469}, posted-at = {2009-10-05 02:33:10}, priority = {2}, title = {Phylogeny.fr: robust phylogenetic analysis for the non-specialist}, url = {http://dx.doi.org/10.1093/nar/gkn180}, volume = {36}, year = {2008} }

TY - JOUR ID - Dereeper2008 L3 - citeulike-article-id:2803275 N2 - 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/ 10.1093/nar/gkn180 IS - suppl_2 JF - Nucl. Acids Res. SN - 1362-4962 AD - Information Génomique et Structurale (IGS), CNRS-UPR2589, IFR-88, Marseille, Méthodes et Algorithmes pour la Bioinformatique (MAB), LIRMM, CNRS – Univ. Montpellier II and Génétique et Evolution des Maladies Infectieuses (GEMI), CNRS – IRD, Montpellier, France. EP - 469 TI - Phylogeny.fr: robust phylogenetic analysis for the non-specialist VL - 36 SP - W465 KW - analyses KW - bioinformatics KW - method KW - phylogenetic KW - phylogeny KW - phyml AU - Dereeper, A AU - Guignon, V AU - Blanc, G AU - Audic, S AU - Buffet, S AU - Chevenet, F AU - Dufayard, JF AU - Guindon, S AU - Lefort, V AU - Lescot, M AU - Claverie, JM AU - Gascuel, O PY - 2008/07/01/ UR - http://dx.doi.org/10.1093/nar/gkn180 ER -