MLHKA- A maximum likelihood ratio test of natural selection, using polymorphism and divergence data.
Please cite Wright, S.I. and Charlesworth, B. 2004. The HKA test revisited: A maximum likelihood ratio test of the standard neutral model. Genetics 168: 1071-1076.
The program is available as the source code (MLHKA_version2.cpp), help file (README.pdf) and sample input file (infile.txt): click HERE to download the files. The source code requires a c++ compliler, e.g. on unix, type: g++ MLHKA_version2.cpp –o MLHKA.
For questions, please e-mail stephen.wright@utoronto.ca
Bug report: August 14, 2007: the previous version of the program, MLHKA.exe, ran into problems calculating likelihoods when divergence values are very high (D>170 or so). Note that most datasets run previously should not be affected, it is ONLY if you had very high divergence values in your analysis. The new version should handle high divergence values correctly. Thanks to Murray Cox for pointing out the problem.