Installation (old page)

What you need to use Bio++
Basically, you need a C++ compiler with STL (Standard Template Library) support, and a text editor. You will need to extract the downloaded archives. Linux comes with the appropriate tools, you will need to install some software under windows (eg 7-zip). You may find useful to use an IDE (Integrated Development environment), particularly under windows.

If you want to retrieve the source from CVS, you'll need a CVS client. From version 1.9.0, bio++ uses the cmake building tool. If it is not directly available on your system, you can download it from here.

Installing pre-compiled version of Bio++ (currently linux only)
Pre-compiled distribution come as two flavors: rpm (RedHat Package Manager) and deb (Debian) packages, for 32 and 64 bits architectures. You can download the packages individually from the repository (see ), or configure your system to automatically fetch them (debian only).

You can find several type of packages: The last category is equivalent to the .tar.gz distribution. The first one provides the dynamic libraries, and is for using program developed using Bio++ and compiled dynamically. The second category is for developing or compiling a program with Bio++. It provides the static libraries and header files. It depends on the packages of the first category.
 * Packages for compiled program use,
 * Packages for development and compilation of programs,
 * Source packages (rpm only).

RPM packages are then installed using the command and DEB packages using the command You will need root access to execute these commands. To install Bio++ locally, you have to install from sources.

Installing Bio++ from source files: the automatic way
This uses an installation file written in bash. start by dowloading it at in a empty directory, and make it executable: The launch it On some systems (Sun for instance), you may need to type instead. The script will check you have all required tools in the right place, download the sources, unpack, configure, compile and install them!

Note: Be sure to have the write access for the installation directory you chosed! In some cases, you will have to run it as super-user.

From the source distribution
Bio++ is distributed via a bundle of source file archives on its website,. For installation under Linux-like systems (Linux, Unix, MacOS X, CygWin), proceed in this way:
 * Download and copy the distribution (.tar.gz files) into a directory where you have writing rights,
 * Decompress each archive file with the command

Using the Version System (Git)
Each library will come in a separate directory.
 * Get yourself into the directory where you want the project files to be.
 * Then retrieve the libraries you need:

Compiling and installing under Linux-like systems
From now, repeat the following steps for each library in the following order:
 * bpp-core
 * bpp-seq
 * bpp-phyl (optional)
 * bpp-popgen (optional)
 * bpp-raa (optional)

The libraries will be installed in /usr/local, a location which requires superuser access rights. An alternative option consists in installing in the user home, for example in a subdirectory called .local. The CMAKE_INSTALL_PREFIX variable specifies where the libraries should be installed.
 * to the source directory,
 * build the Makefile with cmake


 * Build the library:
 * Then install it:
 * You can also generate the API documentation by typing

Note: when installing the other libraries, if you have several versions of the libraries on your system (for instance one in /usr/local/ in addition to your own in $HOME/.local|, you can tell cmake which version to link to by running

Note2: if you are updating a library and encounter compatibility problems for test programs, you should add the option -DBUILD_TESTING=OFF so that new libraries are installed without any compilation of the test programs.

Note3: on some 64bits systems, 64-bits libraries have to be installed in lib64 instead of lib. This can be achieved by passing the -DLIB_SUFFIX=64 option to cmake.