Here is the instructions to compile it if yourself courtesy of the people who made NUPACK.
NUPACK Windows Guide
Following has been validated against windows 7/Server 2008 & Windows 8
NUPACK Source Code can be downloaded here. Note, this version is 3.0.4, however for compilation on Windows an older version(3.0.2) will be required.
******NOTE from Jennifer****** Here is the NUPACK 3.0.2 files https://dl.dropboxusercontent.com/u/87351147/nupack3.0.2.zipInstallation of Cygwin
You will need to download and install Cygwin. Choose the appropriate version for your machine(32/64 bit).
You will be prompted to install Cygwin off of the C: directory
During installation of Cygwin, it is important to select the Development options by double clicking Default next to Devel, switching it to Install.
Installation of Cygwin can take awhile, as many packages are being installed and configured.
After installation, you may encounter a LibUSB warning, and post install script errors, which you can safely ignore. Click OKat the prompt.Compiling NUPACK
Go to wherever you have downloaded the nupack3.0.2 zip file, right click, and then select Extract All.
Press Browse to select Cygwin home directory, which is where we want the extracted contents of nupack3.0.2 to go.
On Windows, NUPACK must be compiled with special command line arguments.
At this point you will need to double click and open Cygwin terminal, where you will be in the home directory. It is important to note that Cygwin is a Unix emulator, and so the following will commands will be UNIX commands.
We will first need to switch into the nupack3.0.2 directory
$ cd nupack3.0.2<br>
Now that we are inside the nupack-3.0.2 folder, we can compile NUPACK using the following command
$ make NUPACK_CFLAGS=-DUSE_DOUBLE
We now need to set an environment variable NUPACKHOME so that other programs(like Multistrand) will be able to find and run the executables. In order to do this we will edit a hidden file, .profile, adding in a line of text. This ensures that the environment variable will be set every time we open Cygwin.
#ensure that you are using >> rather than >, as > will overwrite .profile $ echo "export NUPACKHOME=~/nupack3.0.2" >> .profile #reload the profile for the current session $ source .profile
At this point the NUPACK executables are runnable on your computer.
zip with the files