HaploIHP

HaploIHP - A Program for Haplotype Reconstruction Using Identified Haplotypes and Haplotype Patterns

Program

HaploIHP is developed in the Perl script. The perl script file and the compiled executable file for Windows can be downloaded here.

The package includes the following files (download here):

• • HaploIHP.pl : Perl script file

  • HaploIHP.exe : Executive file of HaploIHP

  • HaploIHP_Manual.pdf : The manual for HaploIHP

  • HaploIHP_Geno.txt : Example genotype data file

  • HaploIHP_HapList.txt: Example initial hapltoype file

  • HaploIHP_HapPattern.txt :Example haplotype pattern file

  • out_freq_example.txt : Example frequency output file

  • out_best_example.txt : Example haplotype assignment file

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 a Perl Script file

• • UNIX or LINUX Systems: Most of LINUX or UNIX system usually have Perl istalled already. Then you can run a Perl script file *.pl and Perl will recognize it. The UNIX or LINUX system will recognize the perl scrip by the first line of the file, which is a path directory starting by '#!'(for example : "#!/usr/bin/perl") . This is the indicator for the path where the Perl is installed. If your UNIx or LINUX system has different path for Perl, change the header accordingly. To find out the correct path for Perl, you may ask your system administrator.

  • WINDOWS : You may need to type "perl" before the perscript file. For example, "perl example.pl".

How to obtain and Install a Perl Interpreter

If you want a Perl interpreter installed, please refer to http://www.perl.org/get.html. You can download a Perl interpreters for your OS system.

Program History

• • February 14, 2007: the program is released.

  • August 16, 2007: the program is modified to incorporate the Partition-Ligation algorithm

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.

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:

Created Date: March 20, 2007

Last Updated Date: Sep 17, 2015