C programs by Jing Hua Zhao

2LD, EH+, FASTEH+, GENECOUNTING, HAP can be put in the same directory with call to the appropriate executables. EH+, FASTEH+ and GENECOUNTING can also share the same parameter and data file. I have tested them extensively under Windows, Sun, Dec Alpha and Linux systems. A brief comparison is shown in the following table. Program MCETDT (Monte Carlo module for the Extended Transmission Disequilibrium Test) is distributed with ETDT and unavailable from this site. Note to enter MS-DOS under the default setup for Windows Visa, you need to run c:\windows\system32\cmd.exe first.

Package name Executable names Documentation Features Limitations
2LD 2ld 2ld.doc, 2ld.htm D’, SE(D’), Cramer’s V for two multiallelic loci, r Requires LDSHELL for many markers, does not show D’ in graphics
EH+ eh, ehplus, fehp, pm, pmplus pm.doc, pm.stm Model-free and permutation tests of allelic association. EH compatible and very easy to use. (having been the top paper in Hum Hered in 2005/6/7). Slower than FASTEH+ and GENECOUNTING but call FASTEH+ for permutation tests from version 1.2
FASTEH+ fpmp,fehp,pfehp fpmp.doc Faster algorithm and likelihood-based LD measures Does not handle missing data, less statistics than EH+
GENECOUNTING gc,gcp,gcx,pgc gc.txt Haplotype frequency estimation and reconstruction, flexible in missing data patterns and X chromosome data, haplotype-specific tests Limited to about 15 SNPs and slow with multiple multiallelic loci with missing data
HAP hap,mia hap.txt Large number of SNPs and multiple imputations, missing data, multiallelic loci Possibly sub-optimal solution