Changes

== Do I always have to sort the pedigree file by marker position?  ==

== Do I always have to sort the pedigree file by marker position?  ==

If you use a reference set of haplotypes, you do not have to as long as the external reference is in correct order. **HOWEVER**, you will probably avoid problems by including markers in the pedigree file sorted in chromosome order.  

If you use a reference set of haplotypes, you do not have to as long as the external reference is in correct order.

== What if I specify ''--states R'' where ''R'' exceeds the maximum possible (2*number diploid individuals - 2 + number_haplotypes)?  ==

== What if I specify ''--states R'' where ''R'' exceeds the maximum possible (2*number diploid individuals - 2 + number_haplotypes)?  ==