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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics
Julien Dutheil1, Sylvain Gaillard, Eric Bazin
1CNRS UMR 5171--Génome, Populations, Interactions, Adaptation (GPIA), Université Montpellier 2, France. Julien.Dutheil@univ-montp2.fr
BMC Bioinformatics
|April 6, 2006
Summary
Bio++ is a C++ library providing object-oriented tools for bioinformatics, accelerating the development of sequence analysis, molecular evolution, and population genetics applications. It offers reusable components for data handling, phylogenetic analysis, and population genomics.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Bioinformatics applications share common needs in data handling and analysis algorithms.
- Reusable libraries can streamline the development of new bioinformatics methods and applications.
Purpose of the Study:
- To present Bio++, a set of object-oriented C++ libraries for bioinformatics.
- To provide efficient and user-friendly components for various bioinformatics tasks.
Main Methods:
- Developed Bio++ as a collection of C++ classes.
- Included components for sequence data, trees, and population genetics datasets.
- Integrated algorithms for phylogenetic and population genetics analyses.
Main Results:
- Bio++ offers classes for data storage, I/O, and sequence manipulation.
- Provides tools for phylogenetic analysis (e.g., maximum parsimony, likelihood).
- Includes functionalities for population genetics/genomics (e.g., diversity statistics, neutrality tests).
Conclusions:
- Bio++ facilitates efficient and user-friendly implementation of bioinformatics methods.
- The library design supports easy extension and development of new algorithms.
- Source code is freely available under the CeCILL license.
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