NGPhylogeny.fr: new generation phylogenetic services for non-specialists

Author:

Lemoine Frédéric12,Correia Damien134,Lefort Vincent3,Doppelt-Azeroual Olivia2,Mareuil Fabien2,Cohen-Boulakia Sarah4ORCID,Gascuel Olivier13

Affiliation:

1. Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France

2. Hub Bioinformatique et Biostatistique, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France

3. Méthodes et Algorithmes pour la Bioinformatique, LIRMM UMR 5506, Université de Montpellier & CNRS, Montpellier, France

4. Laboratoire de Recherche en Informatique, Université Paris-Sud, CNRS UMR 8623, Université Paris-Saclay, Orsay, France

Abstract

Abstract Phylogeny.fr, created in 2008, has been designed to facilitate the execution of phylogenetic workflows, and is nowadays widely used. However, since its development, user needs have evolved, new tools and workflows have been published, and the number of jobs has increased dramatically, thus promoting new practices, which motivated its refactoring. We developed NGPhylogeny.fr to be more flexible in terms of tools and workflows, easily installable, and more scalable. It integrates numerous tools in their latest version (e.g. TNT, FastME, MrBayes, etc.) as well as new ones designed in the last ten years (e.g. PhyML, SMS, FastTree, trimAl, BOOSTER, etc.). These tools cover a large range of usage (sequence searching, multiple sequence alignment, model selection, tree inference and tree drawing) and a large panel of standard methods (distance, parsimony, maximum likelihood and Bayesian). They are integrated in workflows, which have been already configured (‘One click’), can be customized (‘Advanced’), or are built from scratch (‘A la carte’). Workflows are managed and run by an underlying Galaxy workflow system, which makes workflows more scalable in terms of number of jobs and size of data. NGPhylogeny.fr is deployable on any server or personal computer, and is freely accessible at https://ngphylogeny.fr.

Funder

Institut Français de Bioinformatique

INCEPTION project

Publisher

Oxford University Press (OUP)

Subject

Genetics

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