Clustal Omega
1.2.3
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For more information see http://www.clustal.org/
To use libclustalo you will have to include the clustal-omega.h header and link against libclustalo. For linking against libclustalo you will have to use a C++ compiler, no matter if your program was written in C or C++. See below (Using pkg-config / Figuring out compiler flags)) on how to figure out compiler flags with pkg-config.
Assuming Clustal Omega was installed in system-wide default directory (e.g. /usr), first compile (don't link yet) your source (for example code see section Example Source Code) and then link against libclustalo:
Voila! Now you have your own alignment program based on Clustal Omega which can be run with
It's best to use the same compiler that you used for compiling libclustal. If libclustal was compiled with OpenMP support, you will have to use OpenMP flags for you program as well.
Clustal Omega comes with support for pkg-config, which means you can run
to figure out cflags and library flags needed to compile and link against libclustalo. This is especially handy if Clustal Omega was installed to a non-standard directory.
You might have to change PKG_CONFIG_PATH. For example, if you used the prefix $HOME/local/ for installation then you will first need to set PKG_CONFIG_PATH:
To compile your source use as above but this time using proper flags: