Bio++

New version 2.1.0 is out!

Julien Dutheil — 2013-03-15T10:53:29+02:00

We are happy to announce the release of the newest version of the Bio++ libraries, featuring a lot of fixes and improvements, as well as two new libraries dedicated to genomics. Source code and packages are available for download. Check it out, and/or browse the code via the online documentation!

Bio++ Pre-2.1.0 available for testing!

Julien Dutheil — 2012-12-13T09:46:44+02:00

The next release of Bio++ (version 2.1.0) is planned for January 2013. The new release has great new features and two new libraries (bpp-seq-omics and bpp-phyl-omics). The libraries are available on the git repository and are ready to compile! The Bio++ wiki explains how to compile from git http://biopp.univ-montp2.fr/wiki/index.php/Installation. The documentation is also browsable at http://biopp.univ-montp2.fr/apidoc. Packages will be generated at the time of the official release.

New RPM repository

Julien Dutheil — 2012-03-21T14:39:18+02:00

RPM packages are now available for a variety of distributions (Fedora, CentOS, RedHat, Mandriva, Suse) through the openSUSE build service at http://download.opensuse.org/repositories/home:/jdutheil:/Bio++/.

Bio++ 2.0.3 is out!

Julien Dutheil — 2012-03-05T16:07:41+02:00

This new version includes multiple bugis fixed and feature improvements. New packages have been made, notably for the debian and ubuntu linux distributions. In addition, our local repository has been refactored in order to include programs from the Bio++ forge (for instance 'bppsuite', 'comap', or the new 'testnh'). Check the installation page on the wiki for more details!

In addition, some new example files are available for the Bio++ workshop in Bern.

The version which was not one

Julien Dutheil — 2011-06-20T16:09:28+02:00

A new version of Bio++ (2.0.2) has been released. It is however only distributed as debian packages, as it was created mostly for the purpose of testing the integration to debian (see the wiki for more details and http://packages.debian.org/sid/bppsuite for example). A full release (2.0.3), including additional bug fixes will be generated soon.

First patch for version 2.0, new library and more!

Julien Dutheil — 2011-03-15T14:54:32+02:00

We are glad to announce the first patch of the 2.0.0 libraries, including a few bug fixes, but also better packages which should works with all major linux distributions (deb-based and rpm-based). The Bio++ Program Suite packages are now also available on this repository. We also propose a first release of the bpp-qt library, featuring graphical classes. As its names indicates, it links against qt (4). To get a hint on what bpp-qt can do, you can try the Bio++ Phylogenetic Viewer, also proposed for download in its version 0.1.0 (see the Project section for some screenshots). All the libs and programs can also be installed using the bpp-setup.sh script.

Bio++ version 2.0

Julien Dutheil — 2011-02-08T17:39:32+02:00

Bio++ 2.0 is out! It features a lot of new tools and methods, including support for NGS data formats and new powerful sequence evolution models. The increasing amount of code has been reorganized into a new source tree (see the Source Tree page for details). Libraries have been renamed to

bpp-core (the former Utils and NumCalc)
bpp-seq (the former SeqLib)
bpp-phyl (the former PhylLib)
bpp-popgen (the former PopGenLib)
bpp-raa
bpp-qt (still in development)

The sources have migrated to a new Git repository, browsable at http://biopp.univ-montp2.fr/forge/. A new wiki has been set up, where you can find help for using the libraries. Finally, we started to implement unit testing for a better code robustness. The code is checked nightly and the results are reported on the dashboard at http://biopp.univ-montp2.fr/dashboard/. A new bug tracking system was set up, do not hesitate to use it and report errors you main encounter, or features you would like to see implemented http://biopp.univ-montp2.fr/bug/.

New development tools online

Julien Dutheil — 2010-11-12T14:03:01+02:00

The main website underwent a few changes in order to integrate new development tools, namely a bug-tracking system (using MantisDB), project-specific websites using Trac, and a dashboard using CDash. And of course the wiki which is going to supersede the old tutorial and some of the pages on this website (notably installation and configuration help pages).

On the Trac pages of each project, and also on the dashboard, advanced developers will be able to find a link toward the most recent API documentation, nightly built from the Git central repository.

New webserver!

Julien Dutheil — 2010-06-02T13:32:38+02:00

The bio++ website has moved to a new server located at http://biopp.univ-montp2.fr. This server also contains the repository and API documentation. The CVS server will follow soon. A wiki was also created and aims at supersed the aging tutorial. It can be found at http://biopp.univ-montp2.fr/wiki.

Bio++ version 1.9

Julien Dutheil — 2010-04-01T17:30:31+02:00

It took some time, but Bio++ 1.9.0 is finally out! This is the last release before the major changes scheduled for version 2.0. Among the wide set of novelties, this new release brings:

Support for codon models (including non-homogenous models),
Tools for manipulating Hidden Markov Models,
Improved numerical tools (numerical derivatives, parameter transforms...),
A new library, Bio++ RAA (Remote Acnuc Access), allowing you to fetch public databases like GenBank, EMBL or SwissProt,
Algorithms for plotting trees, with support for vector formats like SVG, Fig or LaTeX-PGF.

Bio++ 1.9 also use a new building system, CMake, which should make development on MacOS and Windows easier.