bioinformatics tools written with the Bio++ libraries
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.
07/02/11 Version 0.6.0 available for download, using Bio++ version 2.0.0.
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.
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.
02/03/09 New Bio++ Manual available as html or pdf, see the documentation section for details.
12/12/08 Version 0.3.1 available for download, using Bio++ version 1.7.0.
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.
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).
28/02/08 Version 0.2.2 available. Corrects an important bug in BppReRoot.
08/02/08 Version 0.2.1 available. Corrects an important bug in BppReRoot.
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.
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) Pentium(R) M processor with 1300MHz and 512Mo of SDRAM, with a Linux system. Programs were compiled with static linkage. Check it to see how Bio++ compares to other programs!
BppSuite is available under the CeCILL Open Source license. The source code can be downloaded and compiled (Bio++ needs to be installed). A subversion server is also available from the Gna! webpage project. See here for help.
Packages for linux distributions can be found here (rpm) and here (deb).
An apt-get repository is also available, you can use it by adding the following source:
deb http://download.gna.org/bppsuite/deb/ stable/
to your favorite apt-get manager. Be sure to have added the Bio++ repository too, otherwise this repository will not work!
Finally, a gentoo overlay can be found here.
Alternatively, standalone executables can be downloaded for Linux32,Linux64, Win32 and MacOS (ppc and intel).
Example files are provides with the source distribution, and can be downloaded from here.
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.
Here is a non-exhaustive list of planned extensions: