FreeBSD

An open3dalign executable for FreeBSD can be easily obtained using the GNU C Compiler and ATLAS math libraries.

Firstly, you will have to install Open3DQSAR and its dependencies as described in detail here. Afterwards, you simply need to move to the folder where you have downloaded open3dalign-X.Y.tar.gz, where X and Y are the major and minor version numbers, and build open3dalign:

$ tar -xzf open3dalign-X.Y.tar.gz
$ cd open3dalign-X.Y
$ ./bootstrap
$ ./configure \
        CC=gcc45 \
        CFLAGS="-Wall -O3 -m64 -msse3 -I/build/include \
        -I/build/include" \
        LDFLAGS="-L/build/lib64" \
        --with-atlas \
        --prefix=/build

Clearly, the paths reported in the example above might vary slightly according to your specific installations details.

Subsequently, type

$ make
$ make install

to have the open3dalign executable binary installed in the /build/bin folder and the documentation in /build/share/doc/Open3DALIGN.