epiSNP is a computer package of serial computing programs for genome-wide testing of SNP epistasis and single-locus effects of complex or quantitative traits.

Publications using this software are expected to reference the citation below.


Ma L., H.B. Runesha, D. Dvorkin, J.R. Garbe, and Y. Da. (2008) Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studies. BMC Bioinformatics 9:315. Article URL: http://www.biomedcentral.com/1471-2105/9/315.


epiSNP is available for download. Please contact yda@umn.edu for questions, comments and suggestions.

Operating system Compiler Processor Size Binary
Windows Intel Intel/AMD 5.8 MB epiSNP_v4.2_Windows.zip
Irix SGI MIPS 1.21 MB epiSNP_2.0_SGI_Irix_Mips.tar.gz
Linux (SUSE) Intel AMD 2.85 MB epiSNP_2.0_intel_suse_AMD.tar.gz
Linux (SUSE) Intel Intel (EM64T) 1.96 MB epiSNP_2.0_intel_suse_EM64T.tar.gz
Linux Portland Intel (32 bit) 491 kB epiSNP_2.0_Portland_Linux_Intel.tar.gz
Linux (SUSE) Pathscale AMD 1.21 MB epiSNP_2.0_Pathscale_suse_AMD.tar.gz
Unix (AIX) XLF Power4 820 kB epiSNP_2.0_xlf_AIX_Power.tar
Unix (Solaris) SUN SPARC 1.92 MB epiSNP_2.0_Sun_Solaris_Sparc.tar.gz

The file epiSNP_v4.2_Windows.zip (5.8 MB) has four executable for Windows: EPINET, CPUHD, EPISNPPLOT, and EPINET. Each of the other files has two executables: EPINET and CPUHD. Output files of EPISNP running on Linux or Unix system can be used for EPISNPPLOT and EPINET on a Windows computer.

User Manual

epiSNP Manual 4.2 (PDF, version 4.2)
epiSNP Manual 2.0 (PDF, version 2.0, 154 kB)