This code implements the method in Browning, S., 2006, "Multilocus association mapping using variable length Markov chains", American Journal of Human Genetics, June 2006.  Please cite this paper in any publications resulting from use of the method or code.


Download gzipped tar file containing the R code. This version is dated 12 September 2006 and corrects an error in the drawing routine in the earlier versin.


Unix/Linux instructions:

  gunzip HapVLMC.tar.gz

  tarxvf HapVLMC.tar

Read the README file in the HapVLMC directory for instructions on installing.


The code can be used with R for Windows, however I have not compiled a library, so you would need to “source” each of the files.


New instructions for Windows users:

Here is a zipped library folder: hapVLMC.lib.zip (Note that this is the earlier version that does not correct the error in the draw.graph routine. If you attempt to draw a graph with start.draw>1, the node sizes will be incorrect.)

If you are using Windows, you can use WinZip to unzip the folder hapVLMC.lib, and put it somewhere, for example I put mine in “My Documents”.

After starting R, you can issue a command similar to the following (just change the path to wherever you put your copy of the folder):

library(HapVLMC,lib.loc="C:\\Documents and Settings\\browning\\My Documents\\hapVLMC.lib")

Then you can try commands such as:



and so on… (be aware that the demos take some time)



E-mail me any comments.


A new fast version that can handle hundreds of thousands of markers will be available in a few months.


Back to Sharon Browning’s web page.