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.
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="http://home.gna.org/comap">http://home.gna.org/comap</a>.
- 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="http://home.gna.org/contest">http://home.gna.org/contest</a>.
- Dutheil J. Detecting biochemical constraints throught substitution mapping. JME, 67(3):257-65.
<p>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="http://home.gna.org/figtools">http://home.gna.org/figtools</a>.