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These papers describe the Bio++ libraries:

  • Dutheil J, Boussau B. Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs. BMC Evol Biol. 2008 Sep 22;8(1):255
  • Dutheil J, Gaillard S, Bazin E, Glémin S, Ranwez V, Galtier N, Belkhir K. Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. BMC Bioinformatics. 2006 Apr 4;7:188.

The following works use the Bio++ libraries:

  • Abby SS, Tannier E, Gouy M, Daubin V. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. BMC Bioinformatics. 2010 Jun 15;11:324.
  • Dutheil JY, Ganapathy G, Hobolth A, Mailund T, Uyenoyama MK, Schierup MH. Ancestral population genomics: the coalescent hidden Markov model approach. Genetics. 2009 Sep;183(1):259-74.
  • Nabholz B, Mauffrey J-F, Bazin E, Galtier N, Glémin S. Determination of Mitochondrial Genetic Diversity in Mammals. Genetics. 2008 January; 178(1): 351-361.
  • Scornavacca C, Berry V, Lefort V, Douzery EJ, Ranwez V. PhySIC_IST: cleaning source trees to infer more informative supertrees. BMC Bioinformatics. 2008 Oct 4;9:413.
  • Galtier N. A model of horizontal gene transfer and the bacterial phylogeny problem. Syst Biol. 2007 Aug;56(4):633-42.
  • Dutheil J, Galtier N. Detecting groups of coevolving positions in a molecule: a clustering approach. BMC Evol Biol. 2007; 7: 242.
  • Boussau B, Gouy M. Efficient likelihood computations with nonreversible models of evolution. Syst Biol. 2006 Oct;55(5):756-68.
  • Dutheil J, Pupko T, Jean-Marie A, Galtier N. A model-based approach for detecting coevolving positions in a molecule. Mol Biol Evol. 2005 Sep;22(9):1919-28.