NGPhylogeny.fr: New Generation Phylogenetic Services for Non-specialists

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2019 Apr 28

PMID 31028399

Citations 305

Authors

Frederic Lemoine

Damien Correia

Vincent Lefort

Olivia Doppelt-Azeroual

Fabien Mareuil

Sarah Cohen-Boulakia

Olivier Gascuel

Affiliations

Soon will be listed here.

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.

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