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BMC Bioinformatics. 2006 Apr 4;7:188.

Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics.

Author information

  • 1CNRS UMR 5171--Génome, Populations, Interactions, Adaptation (GPIA), Université Montpellier 2, France. Julien.Dutheil@univ-montp2.fr

Abstract

BACKGROUND:

A large number of bioinformatics applications in the fields of bio-sequence analysis, molecular evolution and population genetics typically share input/output methods, data storage requirements and data analysis algorithms. Such common features may be conveniently bundled into re-usable libraries, which enable the rapid development of new methods and robust applications.

RESULTS:

We present Bio++, a set of Object Oriented libraries written in C++. Available components include classes for data storage and handling (nucleotide/amino-acid/codon sequences, trees, distance matrices, population genetics datasets), various input/output formats, basic sequence manipulation (concatenation, transcription, translation, etc.), phylogenetic analysis (maximum parsimony, markov models, distance methods, likelihood computation and maximization), population genetics/genomics (diversity statistics, neutrality tests, various multi-locus analyses) and various algorithms for numerical calculus.

CONCLUSION:

Implementation of methods aims at being both efficient and user-friendly. A special concern was given to the library design to enable easy extension and new methods development. We defined a general hierarchy of classes that allow the developer to implement its own algorithms while remaining compatible with the rest of the libraries. Bio++ source code is distributed free of charge under the CeCILL general public licence from its website http://kimura.univ-montp2.fr/BioPP.

PMID:
16594991
[PubMed - indexed for MEDLINE]
PMCID:
PMC1501049
Free PMC Article
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