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

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/
Type de document :
Article dans une revue
Nucleic Acids Research, Oxford University Press, 2008, 36 (Web Server), pp.W465-W469. 〈http://www.phylogeny.fr/〉. 〈10.1093/nar/gkn180〉
Liste complète des métadonnées

Littérature citée [24 références]  Voir  Masquer  Télécharger

https://hal-lirmm.ccsd.cnrs.fr/lirmm-00324099
Contributeur : Olivier Gascuel <>
Soumis le : mercredi 24 septembre 2008 - 09:41:34
Dernière modification le : jeudi 24 mai 2018 - 15:59:22
Document(s) archivé(s) le : vendredi 4 juin 2010 - 11:44:27

Fichier

Phylogeny.fr_NAR_2008.pdf
Fichiers produits par l'(les) auteur(s)

Identifiants

Citation

A. Dereeper, Vincent Guignon, G. Blanc, S. Audic, S. Buffet, et al.. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Research, Oxford University Press, 2008, 36 (Web Server), pp.W465-W469. 〈http://www.phylogeny.fr/〉. 〈10.1093/nar/gkn180〉. 〈lirmm-00324099〉

Partager

Métriques

Consultations de la notice

889

Téléchargements de fichiers

407