AntEpiSeeker
About AntEpiSeeker
Epistatic interactions of multiple single nucleotide polymorphisms (SNPs) are now believed to affect individual susceptibility to common diseases. The detection of such interactions, however, is a challenging task in large scale association studies. The ant colony optimization algorithm (ACO) has been shown to be useful in detecting epistatic interactions. AntEpiSeeker, a new two-stage ant colony optimization algorithm, is a powerful and efficient tool for detecting epistasis in a case-control design.

Citation: AntEpiSeeker: detecting epistatic interactions for case-control studies using a two-stage ant colony optimization algorithm. BMC Res Notes 2010, 3: 117.
Download AntEpiSeeker 1.0

Linux Version: AntEpiSeeker1.0_linux.zip

Windows Version: AntEpiSeeker1.0_windows.zip

Source code: AntEpiSeeker1.0_sourcecode.zip

Documentation

Manual

Recompile tips

Results on WTCCC RA data (332,831 markers, 3503 samples):

Chromosome(s)# of SNPsParameter fileWithout minimizing false postiviesMinimizing false positives
All (1-22 plus X)332,831parameters.txtresults_maximized.txtresults.txt
126,097parameters.txtresults_maximized.txtresults1.txt
227,345parameters.txtresults_maximized.txtresults2.txt
323,090parameters.txtresults_maximized.txtresults3.txt
421,115parameters.txtresults_maximized.txtresults4.txt
521,716parameters.txtresults_maximized.txtresults5.txt
621,895parameters.txtresults_maximized.txtresults6.txt
717,680parameters.txtresults_maximized.txtresults7.txt
818,370parameters.txtresults_maximized.txtresults8.txt
915,248parameters.txtresults_maximized.txtresults9.txt
1018,595parameters.txtresults_maximized.txtresults10.txt
1117,637parameters.txtresults_maximized.txtresults11.txt
1216,495parameters.txtresults_maximized.txtresults12.txt
1312,582parameters.txtresults_maximized.txtresults13.txt
1410,312parameters.txtresults_maximized.txtresults14.txt
159,268parameters.txtresults_maximized.txtresults15.txt
1610,105parameters.txtresults_maximized.txtresults16.txt
177,608parameters.txtresults_maximized.txtresults17.txt
189,648parameters.txtresults_maximized.txtresults18.txt
194,317parameters.txtresults_maximized.txtresults19.txt
208,230parameters.txtresults_maximized.txtresults20.txt
214,769parameters.txtresults_maximized.txtresults21.txt
224,097parameters.txtresults_maximized.txtresults22.txt
X6,612parameters.txtresults_maximized.txtresultsX.txt
Contact

Animal Genetics & Bioinformatics Lab

Yupeng Wang: wyp1125@uga.edu

Dr. Romdhane Rekaya: rrekaya@uga.edu