Bio++ Program Suite

bioinformatics tools written with the Bio++ libraries

Bio++ Program Suite Project on Gna! The Bio++ Project

News

26/02/14 The source code of bppsuite has now been migrated to git and can be found on the Bio++ website.

News

01/06/13 Version 0.8.0 available for download, using Bio++ version 2.1.0.

News

29/06/12 Version 0.7.0 available for download, using Bio++ version 2.0.3.

News

15/03/11 Version 0.6.1 available for download, using Bio++ version 2.0.1. Packages are now distributed on the Bio++ repository, along with the library packages. This minor patch only affect packaging, so the 0.6.0 static binaries are unchanged, and were not rebuilt for the 0.6.1 version.

News

07/02/11 Version 0.6.0 available for download, using Bio++ version 2.0.0.

News

02/04/10 Version 0.5.0 available for download, using Bio++ version 1.9.0. The manual was also updated with the new syntax specification.

News

10/06/09 Version 0.4.0 available for download, using Bio++ version 1.8.0. The manual was also updated with the new syntax specification.

News

02/03/09 New Bio++ Manual available as html or pdf, see the documentation section for details.

News

12/12/08 Version 0.3.1 available for download, using Bio++ version 1.7.0.

News

25/09/08 Version 0.3.0 available for download. Several bugs fixed and new +F protein models fully supported. New program BppAncestor to infer ancestral states using ML. Executables are available for Linux (i586 and amd64 architectures), Windows (32 bits) and Mac (PPC and Intel). This version requires Bio++ 1.6.1 to be compiled.

News

26/04/08 Version 0.2.3 available for download. Several bugs fixed and improvements for Non-Homogeneous models (BppSeqGen, BppML). Executables are available for Linux (i586 and amd64 architectures), Windows (32 bits) and Mac (PPC and Intel). If you want to build this version from the source code, you need the development version of Bio++, available from the CVS repository (see the Bio++ website).

News

28/02/08 Version 0.2.2 available. Corrects an important bug in BppReRoot.

News

08/02/08 Version 0.2.1 available. Corrects an important bug in BppReRoot.

Package content

BppDist
Distance matrix estimation and tree reconstruction, under various protein and nucleotides models.
  • Distance estimation (maximum likelihood)
  • Tree reconstruction: U/W PGMA, Neighbor Joining, BioNJ
  • Substitution models: JC69, K80, HKY85, T92, GTR, JTT92, and more
  • Gamma distribution of rates
  • Covarions models
  • Iterative approach to estimate non-topological parameters
  • Non-parametric bootstrap and approximation
BppPars
Parsimony analyses.
  • Tree optimization using Nearest Neighbor Interchanges (NNI) movements
  • Non-parametric bootstrap
BppML
Maximum likelihood analyses.
  • Substitution models: JC69, K80, HKY85, T92, GTR, JTT92, and more, including protein and codon models.
  • Gamma distribution (+ invariant) of rates
  • Covarions models
  • Non homogeneous models, with a very general syntax supporting virtually any possible model.
  • Parameter estimation with various algorithms
  • Tree optimization using Nearest Neighbor Interchanges (NNI) movements
  • Non-parametric bootstrap
  • Site specific rate estimation
BppSeqGen
Sequence simulation (parametric bootstrap).
  • Substitution models: JC69, K80, HKY85, T92, GTR, JTT92, and more, including protein and codon models.
  • Gamma (+ invariants) distribution of rates
  • Covarions models
  • Non homogeneous models, with a very general syntax supporting virtually any possible model.
BppAncestor
Ancestral sequences reconstruction under various models.
  • Substitution models: same as BppML and BppSeqGen, including covarion and non-homogeneous models.
BppSeqMan
Sequence file manipulation.
  • Read / Write to all format available in Bio++
  • Perform translation, transcription, replication, of sequences.
BppConsense
Build consensus trees.
BppPhySamp
Phylogenetic sequences sampler.
Sample sequences from a file, according to a phylogenetic tree or a distance matrix and a user-specified threshold. Keep only one sequence (the longest, or randomly) within clusters of sequences with a distance lower than the threshold.
BppReRoot
Serial re-rooting of trees.
Takes a list of trees as input, and a list of taxa to serve as outgroup. Re-root all the trees in the list according to the specified outgroups.
BppTreeDraw
Drawing phylogenetic trees.
Plot a tree to a file in vector format, so that it can easily be edited afterwards.

Citation

The Bio++ program suite is described in the following paper:
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.

Performance

Programs' output and execution times are provided here, for various models and analyses (BppML only for now). Tests have been performed on a Intel(R) Xeon(R) processor with 2.27GHz and 16Go of RAM, with a Ubuntu 10.04 Linux (64bits) system. Programs were compiled with static linkage. Check it to see how Bio++ compares to other programs!

Availability

BppSuite is available under the CeCILL Open Source license. The source code can be downloaded and compiled (Bio++ needs to be installed). The development version can be found on the git repository:

git clone http://biopp.univ-montp2.fr/git/bppsuite

Previous versions (<= 0.7.0) can be found on the subversion server from the Gna! webpage project. See here for help.

Packages for linux distributions can be found here (rpm) and here (deb). Bpp-Suite is also available through the Bio++apt-get repository, see the Bio++ installation page for instructions.

Alternatively, standalone executables for various platforms can be downloaded at http://biopp.univ-montp2.fr/repos/exe/.

Example files are provided with the source distribution.

Documentation

Example option files provide basic help on the various options of each program. A manual describing available options for all programs can be browsed here and downloaded here. The documentation can also be generated from the source distribution by typing make html and/or make pdf. By default a info file is generated and installed, so that the command info bppsuite will output the manual in a terminal.

You can also find some help on the Bio++ website.

Future developments

Here is a non-exhaustive list of planned extensions:

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