The program hmmcomp implements the method to compare left-right hidden Markov models, e.g. profile hidden Markov models, described in
Metrics and similarity measures for hidden Markov models. Rune B. Lyngsø, Christian N. S. Pedersen and Henrik Nielsen. To appear in Proceedings of the 7th International Conference on Intelligent Systems for Molecular Biology (ISMB), August 1999.
Various extensions to the method implemented in hmmcomp are described in
Measures on hidden Markov models. Rune B. Lyngsø, Christian N. S. Pedersen and Henrik Nielsen. BRICS, Technical Report RS-99-6, April 1999.
The current implementation of hmmcomp is done in C and uses the GNU multiple precision arithmetic library (gmp). To compile hmmcomp you must therefore have a C compiler and a version of gmp installed on your system. The source code gmp-2.0.2.tar.gz to the gmp library is available for free and is straightforward to compile and install.
To install hmmcomp download the source code hmmcomp-1.0.tar.gz and unpack it (tar xzf hmmcomp-1.0.tar.gz), then run make in the subdirectory hmmcomp-1.0 created during unpacking.
The program is used as
hmmcomp [-pv] file1 file2
which compares the hidden Markov models specified in file1 and file2. The format of these files are desribed in the README file distributed together with the source code. The option '-p' determines if a description of the hidden Markov models specified in file1 and file2 is printed. This option is useful to check if the program reads the HMMs the way you think you have describe them. The option '-v' determines how the result of the comparison is presented.