Step 1.  Install Visual Studio C++

Download and install the free visual studio c++ express edition and platform SDK step by step instructions:
http://msdn.microsoft.com/vstudio/express/visualc/usingpsdk/
Installation must be done as a user with admin rights.  Viz studio must be run at least once by an admin after installation to configure paths and registry values.

Alternatively, install a commercial licensed copy of visual studio to do 64-bit and OpenMP builds. 

Step 2.  Install a subversion client

In this example we will use TortoiseSVN:
http://tortoisesvn.tigris.org/
TortoiseSVN requires admin privs to install

Step 3.  Check out Mauve-related source code repositories 

Create a development folder e.g. "C:\Development" and right-click inside the development folder.  Select the "SVN checkout" menu item.  A dialog box will pop up asking the location of the repository to check out, and the destination directory.  Perform a checkout for each of the following repositories:

Step 4.  Install the Boost C++ development libraries

The latest version of boost can be installed with the installers from http://boost-consulting.com .  At present, the latest version is 1.34.1, available here:

http://www.boost-consulting.com/boost_1_34_1_setup.exe  

Alternatively, boost can be built from source.  This may be necessary for 64-bit windows boost builds if the installer does not include them. The following instructions are for the older 1.33.1 release.  Download boost_1_33_1.exe and boost-jam (boost-jam-3.1.13-1-ntx86.zip) from

http://sourceforge.net/project/showfiles.php?group_id=7586

Run the boost self-extracting archive and extract to the development folder (C:\Development).  Extract the bjam binary from the boost-jam zip file to the newly created C:\Development\boost_1_33_1 directory.  Make the changes to vsvars32.bat that are given at the bottom of http://boost.org/tools/build/v1/vc-8_0-tools.html.  Admin privileges are necessary to edit vsvars32.bat, and using "Run As..." on your favorite text editor can be helpful here.  Next, open a command prompt (Start Menu->Run "cmd.exe"), and switch to the boost folder "cd C:\Development\boost_1_33_1".  Start the boost build with the command:
bjam --prefix=C:\Development\boost "-sTOOLS=vc-8_0" install
The build may take hours to complete on a slow machine.  Once completed, the libraries will reside in
C:\Development\boost and the build directories can be deleted (boost_1_33_1\stage and boost_1_33_1\bin) to save disk space.

Step 5.  Configure Visual Studio paths

In order to build mauve-related software, it is necessary to set the include header and library search paths.  To do so, launch visual studio and from the menu bar, select "Tools->Options..."  In the dialog that appears, select the "Projects and Solutions"->"VC++ Directories" panel.  Then select "Show directories for:"->"Include files" in the preference panel.  Now click the new folder icon and add the following directories:

• C:\Development\libGenome
• C:\Development\libClustalW
• C:\Development\muscle
• C:\Development\muscle\libMUSCLE
• C:\Development\libMems
• C:\Development\boost_1_34_1

If source code was installed in a directory other than C:\Development, change the paths accordingly.  Then select directories for library files ("Show directories for:"->"Library files") and add the following paths:

• C:\Development\libGenome\lib
• C:\Development\libClustalW\lib
• C:\Development\muscle\lib
• C:\Development\libMems\lib
• C:\Development\boost_1_34_1\lib

 On 64-bit windows, replace the boost library path with the path to 64-bit libraries, e.g. "C:\Development\boost_1_34_1\lib64"

Step 6.  Build mauveAligner, progressiveMauve, procrastAligner, muscle etc.

Open the file mauveAligner/projects/everything.sln with visual studio.  The workspace contains an assortment of projects related to mauve.  To build all projects, right-click on the text "Solution 'everything'" in the project listing at left and select "Build Solution" from the popup menu.  A batch build can be used to build for several targets at once (menu "Build"->"Batch Build").  When the build succeeds, binaries will generally be in the mauveAligner/projects or mauveAligner/bin directories.