Hidden Markov Models Tool Tutorial

Quick Start:

Start HMMTool

Linux or Unix:
type InstalledDir/HMMTool-1.0/HMMTool

Windows XP:

Navigate to the installed directory, click on HMMTool.bat file not HMMTool.jar file.

Prepare the Data

There are at least two files which you need to provide to the tool. One is input data file, another is its corresponding station information file. We provide a sample stationInfo.txt file and data file under $YourHome/HMMTool-1.0/examples directory. The numbers in stationInfo.txt file are TAB separated not SPACE. The first column in the stationInfo.txt file is station number. The second column is longitude with maximum four decimals. The third column is latitude with maximum four decimals in degrees. Do not use scientific notations for numbers, use decimals. This file should be placed in the same directory as the input data file.

Specify Main Options

No. of Stations, No. of Sequences and Length of Sequences values have to match the input data. User can freely specify No. of Hidden States. The bigger this number, the slower the program runs. If Print to Screen is checked, it will print out results to the screen. See detailed explaination on Examples.

Specify Advanced Options

Click Advanced Options will bring up advanced options window as following.

Launch MVNHMM Tool

Click Launch on main selection panel. It will save all the selections on main window and advanced window to a parameter file, then execute mvnhmm c++ program to generate output file under Output Directory. This will also turn on Graphics menu accordingly. If mvnhmm failed, it will give user a error message box. mvnhmm is developed by Sergey Kirshner. Please follow the link to get more details.