C programs

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). Refman library as of Feb 2005 rmd and rmx)	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

• 2LD
  • full name: Two-locus linkage disequilibrium (LD) calculator
  • description: online documentation and a brief Adobe PDF/Word DOC documentation by Dr David Collier
  • web: 2ld.zip
  • source code language: C
  • systems: PC, Unix (SUN Solaris and Linux)
  • reference:
    • Zhao, J. H. (2004) "2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis". Bioinformatics, 20, 1325-1326
    • Zapata C, Carollo C, Rodriguez S. (2001) "Sampling variance and distribution of the D' measure of overall gametic disequlibrium between multiallelic loci". Annals of Human Genetics, 65, 395-406.
• EH+ or EHPLUS
  • full name: Model-free analysis and permutation tests for allelic association
  • version: 1.0, 1.1, 1.2
  • descriptions: documentation
  • source code language: C
  • web: v 1.0, 1.1, 1.2, 2.0
  • operating systems: PC and Unix (DEC OSF, Sun Solaris, Linux)
  • reference: Zhao, J. H., Curtis, D., Sham, P. C. (2000). "Model-free analysis and permutation tests for allelic associations". Human Heredity, 50(2), 133-139.
• FASTEH+ or FASTEHPLUS
  • full name: faster EH+
  • descriptioin: made available in the spirit of Knuth (1998) with documentation (PDF)
  • web: fehp.zip
  • source code language: C
  • systems: PC, Unix (DEC OSF, SUN Solaris and Linux)
  • reference: Zhao, J. H., Sham, P. C. (2002) "Faster allelic association analysis using unrelated subjects". Human Heredity, 53(1), 36-41.
• GENECOUNTING
  • full name: gene-counting for haplotype analysis with permutation tests for global association and specific haplotypes, accounting for missing data
  • description: executable programs with documentation
  • web: v 1.0, 1.1, 1.2, 1.3, 2.0, 2.1, 2.2
  • source code language: C. A version with source code (for autosomal data) and utility programs can be found in here.
  • systems: PC, Unix (SUN Solaris and Linux)
  • reference:
    • Zhao, J. H, .Lissarrague, S., Essioux, L., Sham, P. C. (2002) "GENECOUNTING: haplotype analysis with missing genotypes" Bioinformatics, 18(12), 1694-1695.
    • Zhao, J. H. (2004) "2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis". Bioinformatics, 20, 1325-1326
• HAP
  • full name: haplotype analysis of polymorphic markers
  • descriptioin: extension of SNPHAP
  • web: v 0.2.1
  • source code language: C
  • systems: PC, Unix (SUN Solaris and Linux)
  • reference: Zhao, J. H. (2004) "2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis". Bioinformatics, 20, 1325-1326