The DOI matches its Crossref record; 34 of the 34 references it cites were found in a registry or an index.
NGPhylogeny.fr: new generation phylogenetic services for non-specialists
Open accessAbstract
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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Cites
Basic local alignment search tool
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms
Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy096 · Cited by 37,529
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
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Self-citationFast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
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Nchioua, R., Kmiec, D., Müller, J. A., Conzelmann, C., Groß, R., Swanson, C. M., Neil, S. J. D., Stenger, S., Sauter, D., Münch, J., et al. (2020) · mBio · doi:10.1128/mbio.01930-20 · Cited by 146
Vazquez, J. M., & Lynch, V. J. (2021) · eLife · doi:10.7554/elife.65041 · Cited by 61
Melgar, A. E., & Zelada, A. M. (2021) · Scientific Reports · doi:10.1038/s41598-021-03066-5 · Cited by 21
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Metadata
- Authors
- Lemoine, F., Correia, D., Lefort, V., Doppelt-Azeroual, O., Mareuil, F., Cohen-Boulakia, S., & Gascuel, O.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-04-27
- Volume
- 47
- Issue
- W1
- Pages
- W260-W265
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2940690307
- Cited by
- 915
- References
- 34
- FWCI
- 23.99
- Type
- journal article
- Language
- en
- Open access
- gold
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