Software available for download
ANCESTRYMAP Version 2.0 is now ready for download. ANCESTRYMAP screens through the genome in a recently mixed population such as African Americans, searching for segments with increased ancestry from one of the ancestral populations, which can indicate the position of disease genes (Patterson et al 2004). ANCESTRYMAP (like the similar Markov Chain Monte Carlo admixture mapping programs ADMIXMAP and MALDSOFT) requires genotyping data from individuals of recently mixed ancestry. To assist in running the program, we have provided a tutorial (online / PDF) and detailed documentation (online / PDF). Source code and executables for running ANCESTRYMAP can be downloaded for either the UNIX or Linux operating systems. For questions write to Arti Tandon (atandon@broad.mit.edu) or Nick Patterson (nickp@broad.mit.edu). We note that this replaces the ANCESTRYMAP version 1.0 release, with various bug fixes and enhancements (what’s new in this version?)
NEW! (January 2008): EIGENSOFT version 2.0 is now available for download. This is the same as EIGENSOFT version 2.0 BETA with a few recent modifications (what's new in EIGENSOFT?). The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Source code, documentation and executables for using EIGENSOFT 2.0 on a Linux platform can be downloaded here. The previous version, EIGENSOFT 1.01, can be downloaded here. For answers to Frequently Asked Questions, see the FAQ. For further questions about the population genetics methodology write to (nickp@broad.mit.edu) and about EIGENSTRAT write to Alkes Price.
SOFTWARE REGISTRATION. We encourage new and existing users of ANCESTRYMAP or EIGENSOFT to register here to assist us in supporting the software (we are trying to maintain an email list of users so that we can send out any information about updates). Registration is voluntary, but would be helpful to us and also to the users.