coraxlib

coraxlib (COre RAXml LIBrary) encapsulates common routines used by likelihood-based phylogenetic software such as raxml-ng. It will eventually supersede both libpll-2 and pll-modules.

Please read the wiki for more information.

Compilation instructions

Please make sure you have CMake 3.0.2 or later installed on your system.

Then, use following commands to clone and build coraxlib:

git clone https://codeberg.org/Exelixis-Lab/coraxlib.git
cd coraxlib
mkdir -p build && cd build
cmake ..
make

If you want to install coraxlib system-wide, please run:

sudo make install

The library will be installed on the operating system's standard paths. For some GNU/Linux distributions it might be necessary to add that standard path (typically /usr/local/lib) to /etc/ld.so.conf and run ldconfig.

Developing with coraxlib

Please see the docs here

coraxlib license and third party licenses

The coraxlib code is currently licensed under the GNU Affero General Public License version 3. Please see LICENSE.txt for details.

coraxlib includes code from several other projects. We would like to thank the authors for making their source code available.

coraxlib includes code from GNU Compiler Collection distributed under the GNU General Public License.

Registering and running tests

We use CTest for manageing our automated tests. You can thus use a standard CMake workflow:

cmake -B build
cmake --build build -j
pushd build && ctest; popd

We use Googletest for our unit tests. To register a new unit-test, create a file in test/unit/src and add the following line to test/unit/CMakeLists.txt:

corax_register_test(test_my_awesome_new_test FILES src/my_awesome_new_test.cpp)
# or
corax_register_test(test_with_custom_defines FILES src/with_custom_defines.cpp DEFINES SAMPLE_DEFINE=1 ANOTHER_DEFINE=2)

On Linear Algebra Libraries

The situation with linear algebra libraries is complicated. To build coraxlib in with non-reversible models enabled, the following needs to be provided in some way:

• CBLAS (a C interface to BLAS)
• LAPACKE (a C interface to LAPACK)

Both of these packages normally depend on BLAS and LAPACK, respectively. Therefore, you will probably need to install all four.

We recommend that users install OpenBLAS. Depending on the package manager, this will provide the interface to all of the above. If this is not the case, then try installing CBLAS and LAPACKE, as these are the final targets required. However, not all BLAS implementations are the same, strictly speaking. If you get linker errors, it is probably due to the installed BLAS implementation not providing "extra" functions, which are present in OpenBLAS.