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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:

  • 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, through 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.


TestNH is a package containing programs to analyse non-homogeneous evolutionary processes. See [1] for more information.


MafFilter is a program for creating pipelines to filter genome alignments. See [2] for more information.


Note: this software is currently not maintained!

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>.