This directory contains some example of how to use allegro. Some of
the examples also run genehunter to compare to the output of
allegro. It is assumed that allegro is in the path of the user, as
well as genehunter, and that they can be run by typing allegro and gh,
respectively.

The following examples are supplied:

ex1         A simple example containing a single sibpair
ex2         An example containing a couple of small families and
            several types of analysis being performed in a single
            run
crossovers  Examples of how the genehunter method of estimating the
            number of crossovers between markers fails
entropy     Example that illustrates how the entropy information
            measure depends on wether the founder couple reduction is
            incorporated, and who is genotyped in a pedigree
f12         A 12 bit family used in the timing experiments in the
            Allegro paper
f18         A 18 bit family used in the timing experiments in the
            Allegro paper
f24         A 24 bit family used in the timing experiments in the
            Allegro paper
floop       A 18 bit family with an inbreeding loop used in the timing
	    experiments in the Allegro paper
