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Julien Y. Dutheil edited this page Sep 17, 2021 · 1 revision

Programs using the Bio++ project:

Table of Contents

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! http://home.gna.org/bppsuite.

CoMap

CoMap is a program that performs substitution mapping procedures and various test for coevolving sites. See CoMap's website on Gna! for more information http://home.gna.org/comap.

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

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 http://home.gna.org/contest.

Published in:

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

TestNH

TestNH is a package containing programs to analyse non-homogeneous evolutionary processes. See http://biopp.univ-montp2.fr/forge/testnh for more information.

MafFilter

MafFilter is a program for creating pipelines to filter genome alignments. See http://biopp.univ-montp2.fr/forge/maffilter for more information.

FigTools

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 http://home.gna.org/figtools.

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