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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
Phylogeny.fr: robust phylogenetic analysis for the non-specialist
A Dereeper1, V Guignon, G Blanc
1Information Génomique et Structurale (IGS), CNRS-UPR2589, IFR-88, Marseille, France.
Nucleic Acids Research
|April 22, 2008
Summary
Phylogeny.fr is a web platform that automates phylogenetic analyses for biologists. It offers flexible modes for both beginners and specialists to reconstruct and visualize evolutionary trees.
Area of Science:
- Evolutionary Biology
- Bioinformatics
- Computational Biology
Background:
- Phylogenetic analyses are crucial in biology, involving sequence alignment, tree reconstruction, and visualization.
- Existing tools often require specialized expertise, posing a barrier for many biologists.
Purpose of the Study:
- To present Phylogeny.fr, an integrated web platform for automating phylogenetic analyses.
- To provide a user-friendly yet sophisticated tool for both novice and expert biologists.
Main Methods:
- The platform chains established bioinformatics tools: MUSCLE for alignment, PhyML for tree building, and TreeDyn for rendering.
- Offers three modes: 'One Click' for simplicity, 'Advanced' for customization, and 'A la Carte' for tailored pipelines.
- Includes BLAST for sequence homology searches and guide trees for neighbor selection.
Main Results:
- Phylogeny.fr streamlines the entire phylogenetic workflow from sequence collection to tree visualization.
- The platform accommodates diverse user needs, from straightforward analyses to complex, customized pipelines.
- Provides accessible and robust phylogenetic analysis for a broad biological audience.
Conclusions:
- Phylogeny.fr enhances accessibility and efficiency in conducting phylogenetic studies.
- The platform empowers biologists to perform sophisticated evolutionary analyses with greater ease.
- Facilitates robust and transparent phylogenetic reconstruction for diverse biological research.
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