maxhap ( A program for estimating rho (4Nr), a crossing-over parameter, and f (= g/r) a gene
This directory has source code and documentation for the program "maxhap" which uses haploid (phased) data. The composite approach is
using a maximum composite likelihood method (Hudson, 2001)).
Hudson, R. R. (2001) Two-locus sampling distributions and their application. Genetics 159: 1805-1817.
Full documentation is in the file readme_hap. This file and the source files are the archive, maxhap.tar.
Download this file and type "tar xvf maxhap.tar", then type "cd maxhapdir", then type "./clmaxhap" and "./clexhap" and you should be
ready to go. (One also needs the tables of two-site configuration probabilities.
These can be found here )
One types "./maxhap" (without arguments) to get a summary of the usage.
Bug warning: The version of exhap available on this site between Mar 15 and Mar 21, 2003, had
a bug. This bug most often led to failure of maxhap (rather than bogus results) but it is possible
that incorrect results could have been produced.