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

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...

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Vydáno v:Nucleic acids research Ročník 47; číslo W1; s. W260 - W265
Hlavní autoři: Lemoine, Frédéric, Correia, Damien, Lefort, Vincent, Doppelt-Azeroual, Olivia, Mareuil, Fabien, Cohen-Boulakia, Sarah, Gascuel, Olivier
Médium: Journal Article
Jazyk:angličtina
Vydáno: England Oxford University Press 02.07.2019
Témata:
Biodiversity
Bioinformatics
Computer Science
Data Structures and Algorithms
Databases, Factual
Information Retrieval
Internet
Life Sciences
Phylogeny
Software
Systematics, Phylogenetics and taxonomy
Web Server Issue
ISSN:0305-1048, 1362-4962, 1362-4962
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Shrnutí: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.
Bibliografie:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
PMCID: PMC6602494
ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkz303