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BMC Bioinformatics

, 7:188

First Online: 04 April 2006Received: 06 December 2005Accepted: 04 April 2006

Abstract

BackgroundA large number of bioinformatics applications in the fields of bio-sequence analysis, molecular evolution and population genetics typically share input-ouput 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.

ResultsWe 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.

ConclusionImplementation 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.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-7-188 contains supplementary material, which is available to authorized users.

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Autor: Julien Dutheil - Sylvain Gaillard - Eric Bazin - Sylvain Glémin - Vincent Ranwez - Nicolas Galtier - Khalid Belkhir

Fuente: https://link.springer.com/







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