Off the top of my head, I know of two programs that can detect errors of
phase. The first is the CHROMPIC option of CRI-MAP which uses maximum
likelihood methods to identify probable phase and will output those
chromosomes with double recombinants. It is usually used with reference
(CEPH) data, but can handle general pedigrees, if the disease phenotype
can be assumed as a simple single gene. I don't know how well it will work
if there are many missing (untyped) individuals in the pedigree.
The second program is CHROMLOOK, but it probably is not appropriate,
since it requires the families to be broken down into individual sibships,
and expects both parents to be typed (e.g. like CEPH pedigrees). However,
I personally think it has better output (then again, I would since I
wrote it!). It uses non-likelihood methods to assume phase.
Jonathan Haines
