How To Build 64-bit Clustal Omega on Windows
Clustal Omega binaries are available for several platforms. However, Windows binary is 32-bit only and there is no information to build 64-bit binary in the package.
We tried to build Clustal Omega ver.1.2.0 for 64-bit Windows 7.
Up-to-date as of 10/14/2014
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1. Preparation
1.1. Install free MinGW64 on Windows 7.  Download from targetting Win64/Personal Builds/sezero_4.5_20111101/, extract it, move mingw64 folder to C:\ and rename it to mingw. MinGW64 provides tools to develop 64-bit Windows applications using gcc and g++. With MinGW64, some software developed for Linux platform can be built on Windows.
1.2. There is a file named in C:\mingw folder. Extract it under C:\mingw folder.
1.3. Download MSYS-1.0.11.exe from and install it.
1.4. Download Clustal Omega source from
1.5. Copy downloaded file to MSYS.  If you installed MSYS in C:\msys and your account is Administrator, copy it to C:\msys\1.0\home\Administrator. You can do it using Windows explorer.
1.6. Download argtable2-13.tar.gz from and copy it to MSYS. This is required by Clustal Omega.
2. Configuration and Build process
2.1. Launch MSYS and extract argtable2 source as tar xfz argtable2-13.tar.gz.
2.2. Extract Clustal Omega source as tar xfz clustal-omega-1.2.0.tar.gz.
2.3. cd argtable2-13; ./configure; make; make install
2.4. cd ~/clustal-omega-1.2.0
2.5. ./configure CFLAGS='-I/usr/local/include -DSRE_STRICT_ANSI' LDFLAGS='-L/usr/local/lib'
2.6. make; make install
2.7. You can find clustalo.exe in /usr/local/bin folder which is C:\msys\1.0\local/bin.
2.8. Following DLLs are necessary to run clustalo.exe.  Put them in the same folder where clustalo.exe exists. C:\mingw\bin\libcc_sjlj-1.dll, C:\mingw\bin\libgomp-1.dll, C:\mingw\bin\libstdc++-6.dll, C:\mingw\bin\pthreadGC2-w64.dll
3. Pre-built binary
3.1. If you want pre-built binary, please send email to .