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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| Published in: | Nucleic acids research Vol. 47; no. W1; pp. W260 - W265 |
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| Main Authors: | , , , , , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
England
Oxford University Press
02.07.2019
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| Subjects: | |
| ISSN: | 0305-1048, 1362-4962, 1362-4962 |
| Online Access: | Get full text |
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| 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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| AbstractList | 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. 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.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. Phylogeny.fr, created in 2008, has been designed to facilitate the execution of phylogenetic workflows, and is nowadays widely used. However, since its de- velopment, 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 devel- oped 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 stan- dard methods (distance, parsimony, maximum like- lihood and Bayesian). They are integrated in work- flows, 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. |
| Author | Doppelt-Azeroual, Olivia Lefort, Vincent Correia, Damien Lemoine, Frédéric Cohen-Boulakia, Sarah Gascuel, Olivier Mareuil, Fabien |
| AuthorAffiliation | 4 Laboratoire de Recherche en Informatique, Université Paris-Sud, CNRS UMR 8623, Université Paris-Saclay, Orsay, France 1 Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France 3 Méthodes et Algorithmes pour la Bioinformatique, LIRMM UMR 5506, Université de Montpellier & CNRS, Montpellier, France 2 Hub Bioinformatique et Biostatistique, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France |
| AuthorAffiliation_xml | – name: 4 Laboratoire de Recherche en Informatique, Université Paris-Sud, CNRS UMR 8623, Université Paris-Saclay, Orsay, France – name: 2 Hub Bioinformatique et Biostatistique, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France – name: 1 Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France – name: 3 Méthodes et Algorithmes pour la Bioinformatique, LIRMM UMR 5506, Université de Montpellier & CNRS, Montpellier, France |
| Author_xml | – sequence: 1 givenname: Frédéric surname: Lemoine fullname: Lemoine, Frédéric organization: Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France, Hub Bioinformatique et Biostatistique, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France – sequence: 2 givenname: Damien surname: Correia fullname: Correia, Damien organization: Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France, Méthodes et Algorithmes pour la Bioinformatique, LIRMM UMR 5506, Université de Montpellier & CNRS, Montpellier, France, Laboratoire de Recherche en Informatique, Université Paris-Sud, CNRS UMR 8623, Université Paris-Saclay, Orsay, France – sequence: 3 givenname: Vincent surname: Lefort fullname: Lefort, Vincent organization: Méthodes et Algorithmes pour la Bioinformatique, LIRMM UMR 5506, Université de Montpellier & CNRS, Montpellier, France – sequence: 4 givenname: Olivia surname: Doppelt-Azeroual fullname: Doppelt-Azeroual, Olivia organization: Hub Bioinformatique et Biostatistique, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France – sequence: 5 givenname: Fabien surname: Mareuil fullname: Mareuil, Fabien organization: Hub Bioinformatique et Biostatistique, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France – sequence: 6 givenname: Sarah orcidid: 0000-0002-7439-1441 surname: Cohen-Boulakia fullname: Cohen-Boulakia, Sarah organization: Laboratoire de Recherche en Informatique, Université Paris-Sud, CNRS UMR 8623, Université Paris-Saclay, Orsay, France – sequence: 7 givenname: Olivier surname: Gascuel fullname: Gascuel, Olivier organization: Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France, Méthodes et Algorithmes pour la Bioinformatique, LIRMM UMR 5506, Université de Montpellier & CNRS, Montpellier, France |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/31028399$$D View this record in MEDLINE/PubMed https://hal.science/hal-02341225$$DView record in HAL |
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