This is actually a suite of macros that will format data from an Excel spreadsheet to a format ready to be used by the program "Arlequin", which will reconstruct haplotype frequencies within the population, based on the genotypes given. After which, other macros will extract the haplotype information, calculate linkage disequilibrium between markers, and prepare an input sheet for the "GOLD" program, which makes a graphical display of this data. Then, a last macro can reconstruct the haplotypes of each individual in the population, using a maximum likelihood method and the haplotypes present in the population as proposed by Arlequin. I have now added a way to make input sheets to use David Clayton's htSNP program to do "Haplotype Tagging".
The supplemental concerning the validation of the haplotype reconstruction can be found here.
The recently discovered bug concerning haplotype reconstruction when more than 9 alleles are present for a polymorphism has been fixed (I hope). If you run into a problem, be sure to let me know!
Arlequin can be downloaded from: http://lgb.unigene.ch/arlequin/
GOLD can be downloaded from : http://www.sph.umich.edu/csg/abecasis/GOLD/
David Clayton's STATA program can be downloaded from: http://www-gene.cimr.cam.ac.uk/clayton/
Platforms tested:
Windows 98, NT4, ME, 2000
Runs in Excel 98 and 2000.
This macro has been developed by David Cox.
Please use the tools available at The
Macroshack at bioinformatics.org
for comments, suggestions, and bugs.
Instructions on using the macro.
Download the macro.
Back to the program list.
This page was last updated on: August 28, 2002 by David G. Cox