mutpath is designed to interface with the BEAST phylogenetics package, so you will obviously want to install BEAST. The actual mutational path mapping requires the Markov Jumps feature of BEAST. This feature is not available in the current stable release of BEAST (this may change when version 1.8 is released), so you need to obtain the developer’s version of BEAST (or perhaps version 1.8, I have not tested that). Use of the Markov Jumps feature also requires using the BEAGLE library, so you need to install that as well.
Here are the commands that I used to obtain BEAST (v1.8.0pre Prelease r5356) and BEAGLE (revision 1093) on my computer. For BEAST:
svn co http://beast-mcmc.googlecode.com/svn/trunk BEAST
cd BEAST
ant
java -jar build/dist/beast.jar
And for BEAGLE:
svn co http://beagle-lib.googlecode.com/svn/trunk BEAGLE
cd BEAGLE/
./autogen.sh
./configure
make
sudo make install
make check
If you just want to install BEAGLE locally in some directory such as BEAGLE_libs, use:
./configure --prefix ~/BEAGLE_libs
and then you can install without the sudo command.