%0 Journal Article
%T Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics
%A Julien Dutheil
%A Sylvain Gaillard
%A Eric Bazin
%A Sylvain Gl¨Śmin
%A Vincent Ranwez
%A Nicolas Galtier
%A Khalid Belkhir
%J BMC Bioinformatics
%D 2006
%I BioMed Central
%R 10.1186/1471-2105-7-188
%X 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.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 webcite.The design of re-usable software components into libraries has proved to be useful to the rapid development of bioinformatics applications, as witnesses the success of the ever growing open source libraries known as the Bio{*} projects. These libraries cover many fields of bioinformatics, but rarely offer tools for intensive calculus, as required for phylogenetic analyses for instance. Such computer-expensive applications are usually written in C, a compiled low-level language. Programming time-consuming tasks often requires the implementation of specific algorithms optimized for each particular problem. However, despite these specifities, there are some common points (e.g. likelihood calculation, minimization), and developers will appreciate to use modules pre-programmed in a flexible manner.The use of the C++ language combines both the computer efficiency of the C language and the convenience of
%U http://www.biomedcentral.com/1471-2105/7/188