{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T06:19:30Z","timestamp":1777702770102,"version":"3.51.4"},"reference-count":14,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2006,12]]},"abstract":"Abstract<\/jats:title>\n \n Background<\/jats:title>\n A 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.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n 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.<\/jats:p>\n <\/jats:sec>\n \n Conclusion<\/jats:title>\n 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<\/jats:ext-link>.<\/jats:p>\n <\/jats:sec>","DOI":"10.1186\/1471-2105-7-188","type":"journal-article","created":{"date-parts":[[2006,4,20]],"date-time":"2006-04-20T14:20:53Z","timestamp":1145542853000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":93,"title":["Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics"],"prefix":"10.1186","volume":"7","author":[{"given":"Julien","family":"Dutheil","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sylvain","family":"Gaillard","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"Bazin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sylvain","family":"Gl\u00e9min","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vincent","family":"Ranwez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicolas","family":"Galtier","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Khalid","family":"Belkhir","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2006,4,4]]},"reference":[{"key":"927_CR1","doi-asserted-by":"publisher","first-page":"2325","DOI":"10.1093\/bioinformatics\/btg316","volume":"19","author":"K Thornton","year":"2003","unstructured":"Thornton K: Libsequence: a C++ class library for evolutionary genetic analysis. 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