The Exelixis Lab

Enabling Research in Evolutionary Biology

OmegaPlus Population Genetics code

A parallel tool for rapid and scalable detection of selective sweeps in whole-genome datasets

When using this code please cite the following two papers: Bioinformatics application note and parallelization

OmegaPlus is a scalable implementation of the omega-statistic (Kim and Nielsen 2004) to detect selective sweeps in whole-genome data based on linkage disequilibrium patterns.

OmegaPlus has been tested with fully phased data, but also with unphased data, where we can determine to which diploid individual a SNP belongs to, but we can not determine which of the two chromosomes carries the SNP.

Outgroup information is not required. The program recognizes FASTA, Hudson's ms-like, and MaCS-like ( formats.

OmegaPlus can scan the DPGP dataset (, reference release 1.0 September 2009, 37 sequences and ~340,000 SNPs) for positive selection in 55 seconds.

In addition to the efficient sequential implementation, we provide three parallelized versions that use fine-, coarse-, and multi-grain parallelism. Right now this is a pure command-line tool, available for Windows and Linux operating systems.

We strongly recommend to use the LINUX version of OmegaPlus.
Note that only limited support will be provided for the Windows version.
For compiling the code, GCC version 4.4 or greater is recommended. For gcc versions prior to version 4.4 please remove the optimization flag (-O3) from the Makefiles before compiling the code. When OmegaPlus is compiled with older gcc versions it will yield different results on identical input data compared to the ouput it generates when -O3 is activated. This is most probably due to some to aggressive optimizations under -O3.

Many thanks to Stefan Laurent (LMU Munich) for pointing this out.

Download the most recent GNU GPL Linux version 2.2.2 here , it includes a bug fix in the VCF file parser that was associated with handling missing data.

Download GNU GPL Windows version here

Download the manual here

Examples are provided with the source code (see directory "examples").

If you have questions or you would like to report a bug, please register at the OmegaPlus google group (
or send an email to or