HaploHMM - A Hidden Markov Model (HMM) Based Program for Haplotype Inference
Using Identified Haplotypes and Haplotype Patterns
Program
HaploHMM is developed using C++ and the compiled executable file for Windows operating system can be downloaded here.
The package includes the following files (download here):
HaploHMM.exe : Executive file of HaploHMM
HaploHMM_Manual.pdf : The manual for HaploHMM
HaploHMM_Geno.txt : Example genotype data file
HaploHMM_HapList.txt : Example initial hapltoype file
HaploHMM_HapPattern.txt : Example haplotype pattern file
HaploHMM_res.txt : an example file for haplotypes of each individual
HaploHMM_res.sample11 : an example file for haplotypes of each individual sampled at the HMM iteration 11.
After downloading the package, unzip it and copy all files into the same file folder. The manual (PDF format) for how to use this program can also be downloaded here.
How to run HaploHMM
HaploHMM.exe runs on the Command Promote window of Microsoft Windows operating system. Here we use Microsoft Windows 7 operating system to show how we can run HaploHMM.
To run HaploHMM, you first need to open a Command Prompt window. There are two ways to do this. The first way is to click the Start button, click All Programs , click Accessories , and then click Command Prompt . The second way is to click Start button, type Command Prompt in the Search box, then double-click Command Prompt in the list of results.
After a Command Promote window is opened, change the folder to the folder that contains your program and data, then type the command with the options followed by the specified value for each option. Please refer to the program manual for the details.
Program History
June 22, 2014: the program is released.
References
Yoo Y, Kaslow R, Tang J, Zhang K. 2007. Haplotype inference for present-absent genotype data for clustered genes using identified haplotypes and haplotype patterns. Bioinformatics, 23: 2399-2406.
Jihua Wu, Guo-Bo Chen, Degui Zhi, Nianjun Liu, Kui Zhang. 2014. A hidden Markov model for haplotype inference for present-absent data of clustered genes using identified haplotypes and haplotype patterns. Frontiers in Statistical Genetics. Under Review.
We are planning to update our program regularly. You are welcome to suggest features that you want us to implement into this program. We greatly appreciate if you could point out any bugs when you use our program. Our contact information is:
Kui Zhang, Ph.D.
Department of Mathematical Sciences
Michigan Technological University
1400 Townsend Drive
Houghton, Michigan 49931
Phone: 906-487-2918
Fax: 906-487-3133
Email: kuiz@mtu.edu
Created Date: June 22, 2014
Last Updated Date: June 22, 2014