{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T17:33:10Z","timestamp":1781285590018,"version":"3.54.1"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2019,4,27]],"date-time":"2019-04-27T00:00:00Z","timestamp":1556323200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Institut Fran\u00e7ais de Bioinformatique","award":["ANR-11-INBS-0013"],"award-info":[{"award-number":["ANR-11-INBS-0013"]}]},{"name":"INCEPTION project","award":["PIA\/ANR-16-CONV-0005"],"award-info":[{"award-number":["PIA\/ANR-16-CONV-0005"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>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 (\u2018One click\u2019), can be customized (\u2018Advanced\u2019), or are built from scratch (\u2018A la carte\u2019). 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.<\/jats:p>","DOI":"10.1093\/nar\/gkz303","type":"journal-article","created":{"date-parts":[[2019,4,17]],"date-time":"2019-04-17T12:33:50Z","timestamp":1555504430000},"page":"W260-W265","source":"Crossref","is-referenced-by-count":850,"title":["NGPhylogeny.fr: new generation phylogenetic services for non-specialists"],"prefix":"10.1093","volume":"47","author":[{"given":"Fr\u00e9d\u00e9ric","family":"Lemoine","sequence":"first","affiliation":[{"name":"Unit\u00e9 Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France"},{"name":"Hub Bioinformatique et Biostatistique, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Damien","family":"Correia","sequence":"additional","affiliation":[{"name":"Unit\u00e9 Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France"},{"name":"M\u00e9thodes et Algorithmes pour la Bioinformatique, LIRMM UMR 5506, Universit\u00e9 de Montpellier & CNRS, Montpellier, France"},{"name":"Laboratoire de Recherche en Informatique, Universit\u00e9 Paris-Sud, CNRS UMR 8623, Universit\u00e9 Paris-Saclay, Orsay, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vincent","family":"Lefort","sequence":"additional","affiliation":[{"name":"M\u00e9thodes et Algorithmes pour la Bioinformatique, LIRMM UMR 5506, Universit\u00e9 de Montpellier & CNRS, Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivia","family":"Doppelt-Azeroual","sequence":"additional","affiliation":[{"name":"Hub Bioinformatique et Biostatistique, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabien","family":"Mareuil","sequence":"additional","affiliation":[{"name":"Hub Bioinformatique et Biostatistique, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7439-1441","authenticated-orcid":false,"given":"Sarah","family":"Cohen-Boulakia","sequence":"additional","affiliation":[{"name":"Laboratoire de Recherche en Informatique, Universit\u00e9 Paris-Sud, CNRS UMR 8623, Universit\u00e9 Paris-Saclay, Orsay, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivier","family":"Gascuel","sequence":"additional","affiliation":[{"name":"Unit\u00e9 Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France"},{"name":"M\u00e9thodes et Algorithmes pour la Bioinformatique, LIRMM UMR 5506, Universit\u00e9 de Montpellier & CNRS, Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,4,27]]},"reference":[{"key":"2019062808123965100_B1","doi-asserted-by":"crossref","first-page":"W465","DOI":"10.1093\/nar\/gkn180","article-title":"Phylogeny. fr: robust phylogenetic analysis for the non-specialist","volume":"36","author":"Dereeper","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2019062808123965100_B2","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. 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