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.
Multiple alignment applications installation
These instructions show how to install the HMM application on
- Download the file setup.exe (12 MB)
to some folder on your PC.
- 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
- When the installation is completed, double click on icon created on
your desktop, it will labeled Math127.
- Now you will see 2 icons that represent 2 tools. One for the HMM
application and another for a multiple alignment application.
- 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
symbols 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