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".
IMPORTANT! I am currently working on a new version of PHARE that will work with the latest version of PHASE. I am also updating it to work with Dan Stram’s program, and will upload the entire thing when complete. I can’t guarantee when this will be done, so if you need to use the new version of PHASE, send me an email, and I’ll try to help you out.
Also, there are new problems with extracting data from Arlequin. I think this is due to differences in how Excel opens html files. I haven’t had much of a chance to look into this yet due to time constraints, so please be patient if you are running into trouble.
My haplotyper has evolved into PHARE, which can use two other methods of haplotype reconstruction, PHASE and Haplotyper.
PHASE can be found at http://www.stats.ox.ac.uk/mathgen/software.html
Haplotyper can be found at http://www.people.fas.harvard.edu/~junliu/ and a user agreement to be used, which is free for academic institutions.
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/
Windows 98, NT4, ME, 2000
Runs in Excel 98 and 2000.
Dr. Alex Doney in Dundee, Scotland, has run into some problems with Windows XP. The macro may not be compatible with this OS, so please, let me know if you are using XP and it works....
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: November 12, 2002by David G. Cox