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

作者：Alexis Dereeper, Valentin Guignon, Guillaume Blanc, Stéphane Audic, Sylvain Buffet, François Chevenet, Jean-François Dufayard, Stéphane Guindon, Vincent Lefort, Magali Lescot, Jean‐Michel Claverie, Olivier Gascuel · 发表于：Nucleic Acids Research · 年份：2008 · DOI：10.1093/nar/gkn180 · 被引用次数：4817 · 研究领域：Genomics and Phylogenetic Studies、Plant Diversity and Evolution、Plant Taxonomy and Phylogenetics

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 s...