Skip Navigation
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.


The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Internet Explorer is no longer a supported browser.

This website may not display properly with Internet Explorer. For the best experience, please use a more recent browser such as the latest versions of Google Chrome, Microsoft Edge, and/or Mozilla Firefox. Thank you.

Your Environment. Your Health.

Correlation-Based Tests

Correlation-Based Tests for Phase Unknown Linkage Disequilibrium & Contingency Tables

The programs here are to accompany Zaykin, DV, Pudovkin AI, Weir BS 2008. Correlation-based inference for linkage disequilibrium with multiple alleles. Genetics (in press). They are compiled for Windows' "Command Line". The C++ source, developed under Linux (GNU compiler), is also provided.  

  • dz-rxc.exe -- computes correlation-based tests for RxC contingency tables (as well as several other tests)
  • mcld.exe -- computes correlation-based tests for linkage disequilibrium. A sample input file is "loci.txt" in this directory (this file is modeled after LD found in STRs in Rosenberg NA et al., Science 2002; 298:2981-2985)


  • Zipped file containing the C++ source, exe and txt documents: (396KB) Updated: 2010/01/13
  • For support: please contact Dmitri Zaykin("/Rhythmyx/assembler/render?sys_contentid=35225&sys_revision=5&sys_variantid=1278&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="1278" sys_dependentid="35225" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="35225" sys_siteid="" sys_folderid="")


  1. Start the "Command Prompt" window. (In Windows XP it is in Programs -> Accessories -> Command Prompt)
  2. Change to the directory where you stored the programs, e.g. type "cd C:\MyStuff"
  3. Run one of the programs to get help screen on its usage, e.g. type at the prompt "dz-rxc.exe" or "mcld.exe"
  4. To run sample files downloaded from this directory, type "mcld.exe -file=loci.txt" or "dz-rxc.exe 10000 < rxcdat.txt"
  5. you can direct output to a file as e.g. "dz-rxc.exe 10000 < rxcdat.txt > Results.txt"


Dmitri V. Zaykin, Ph.D.
Principal Investigator
Tel 984-287-3694
to Top