Detail tutorial at http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014
Intersting bookmark Jit, you can also try Recombination Detection Program (RDP) http://web.cbio.uct.ac.za/~darren/rdp.html
Using population genomic data http://arxiv.org/ftp/arxiv/papers/1403/1403.4264.pdf to detect recombination hotspot.