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12:00
A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
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NGPhylogeny.fr: new generation phylogenetic services for non-specialists
Frédéric Lemoine1,2, Damien Correia1,3,4, Vincent Lefort3
1Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France.
Nucleic Acids Research
|April 28, 2019
Summary
NGPhylogeny.fr offers a flexible, scalable platform for phylogenetic analysis, integrating the latest tools and methods. This refactored system enhances usability for diverse evolutionary biology research needs.
Area of Science:
- Evolutionary Biology
- Bioinformatics
Background:
- Phylogeny.fr, established in 2008, is a widely used platform for phylogenetic workflows.
- Evolved user needs, new tools, and increased job volume necessitated a platform upgrade.
Purpose of the Study:
- To refactor Phylogeny.fr into a more flexible, scalable, and user-friendly platform named NGPhylogeny.fr.
- To integrate a comprehensive suite of updated and novel phylogenetic tools and methods.
Main Methods:
- NGPhylogeny.fr integrates numerous up-to-date phylogenetic tools (e.g., TNT, FastME, MrBayes, PhyML, trimAl).
- It supports diverse applications including sequence searching, multiple sequence alignment, model selection, and tree inference.
- Workflows are managed by the Galaxy workflow system for enhanced scalability.
Main Results:
- The platform offers flexible workflow configurations: 'One click', 'Advanced', and 'A la carte'.
- NGPhylogeny.fr supports a wide range of phylogenetic methods (distance, parsimony, maximum likelihood, Bayesian).
- It is deployable on various servers and personal computers.
Conclusions:
- NGPhylogeny.fr provides a significantly enhanced and scalable solution for modern phylogenetic analyses.
- The platform's flexibility and comprehensive tool integration cater to evolving research demands in evolutionary biology.
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