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Programs using the Bio++ project

Bio++ Program Suite

This software suite contains several example programs that use various methods from the libraries. The suite currently contains five programs:

  • bppDist: Distance matrix computation and tree reconstruction using various methods and models.
  • bppPars: Parsimony score computation and tree optimization + bootstrap.
  • bppML: Maximum likelihood computation and tree optimization + bootstrap.
  • bppSeqGen: Sequence simulations under various models of evolution.
  • bppConsense: Tree consensus methods and bootstrap values computations.
  • bppSeqMan: Sequence manipulation, including file format conversion.
  • bppPhySamp: Phylogenetic Sampler: sample sequences according to a phylogenetic tree or a distance matrix.
  • bppReRoot: Reroot a set of tree from a file according to a list of taxa.
  • bppAncestor: Reconstruct ancestral states and rates using any supported model of substitution.
  • bppTreeDraw: Plot trees in various vector formats.

Executable, source code, documentation and example file are available on BppSuite's page on Gna! <a href=""></a>.</p>


CoMap is a program that performs substitution mapping procedures and various test for coevolving sites. See CoMap's website on Gna! for more information <a href=""></a>.

Published in:<p>

  • Dutheil JY, Jossinet F, Westhof E. Base pairing constraints drive structural epistasis in ribosomal RNA sequences. Mol Biol Evol. 2010 (ahead of print).
  • Dutheil J, Galtier N. Detecting groups of coevolving positions in a molecule: a clustering approach. BMC Evol Biol. 2007 Nov 30;7:242.
  • 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


ConTest is a program that detects sites within a protein alignment that are under biochemical constraint, throught substitution mapping. See ConTest's website on Gna! for more information <a href=""></a>.

Published in:

  • Dutheil J. Detecting biochemical constraints throught substitution mapping. JME, 67(3):257-65.


This pakage contains two programs, seqfig and treefig that generate sequence and tree plots in vector format.

See FigTools' website on Gna! for more information <a href=""></a>.