To install cmake is needed. Cmake can be downloaded from http://www.cmake.org/HTML/Download.html.
gengetopt version 2.22 is also needed 


For installation of modhmm:

mkdir /tmp/build
cd /tmp/build
cmake -D CMAKE_INSTALL_PREFIX=/my/install/dir  /this/source/dir
make
make install






Directory layout

src/blastscripts    --   blastparsing scripts
src/c               --   modhmmt, modhmms
src/data            --   replacement matrix
src/docbook         --   documentation
src/java            --   modhmmc
