Hidden Markov Models and Multiple Alignment

Nasser M. Abbasi. 2002

This page contains information about the Hidden Markov Models final project report and matlab tool that I have written in 2002. This page also contains information how to download the windows executable and install it on your PC.


  1. HTML
  2. PDF

Multiple alignment applications installation

These instructions show how to install the HMM application on windows.
  1. Download the file setup.exe (12 MB) to some folder on your PC.
  2. Once setup.exe is downloaded, Double click on it to run it. This will bring up a standard installation. Click next on the questions being asked.
  3. When the installation is completed, double click on icon created on your desktop, it will labeled Math127.
  4. Now you will see 2 icons that represent 2 tools. One for the HMM application and another for a multiple alignment application.
  5. To run either application, double click on the icon. This will bring up the application.

Instruction for running HMM

Double click on the HMM icon as per the above instruction.

Now the main screen will come up

Now click the

Open HMM configuration file
to open the HMM file that describes the system being modeled. I include few files with this installation. Navigate as follows to find the files
and select the file report_example.

Now enter the observation sequence in the window (type the sequence). The sequence must contain symbols that belong to the allowed set of symbols as shown in the

window. For the report_example, these are A and C and T only. So you can type in ACCCCTTT for example.

Now hit the RUN botton on the upper right hand corner. This is the result

This is also the README.txt file I worte for the installation

source code listing

  1. getPosOfState.m.txt
  2. nma_hmmBackward.m.txt
  3. nma_hmm_callbacks.m.txt
  4. nma_hmmEmitProb.m.txt
  5. nma_hmmForward.m.txt
  6. nma_hmmGUI.m.txt
  7. nma_hmm_main.m.txt
  8. nma_hmm_veterbi.m.txt
  9. nma_logOfSumsBeta.m.txt
  10. nma_logOfSums.m.txt
  11. nma_readHMM.m.txt
  12. nma_trim.m.txt