Several people requested the answers to my query about software for  
conveniently reconstructing the genotypes at each locus of the parents  
of a full sibship.  Here is a summary of what I learned.

MY ORIGINAL QUESTION:
Hi,
  Has anyone written a script to choose the most likely genotypes of  
the two parents of a full-sibship from the genotypes of those  
siblings?  Here I want to pre-specify the sibships and just  
reconstruct the most likely parental genotypes at each locus.
Thanks,
Mike

RECOMMENDATIONS:

Ian Wilson's PARENTAGE program seems like the best way to go. It will  
also do sibship partitions with genotyping error and a number of other  
useful procedures.

PEDIGREE (http://herbinger.biology.dal.ca:5080/Pedigree/) will do the  
trick but extracting your parental genotypes out of the output is very  
labor intensive if you have a large number of sibships.

Note that if you want to write your own script, the equations for  
estimating the most likely parental genotypes of a full sibship are  
presented in table 2 of Banks et al., 2000. Canadian Journal of  
Fisheries and Aquatic Sciences 57:915-927.

Several people recommended COLONY but I don't think it will actually  
reconstruct both parental genotypes (at least the latest version  
won't) - if you try it, you'll see that it identifies both parents as  
having the same genotype.  If I'm wrong about this, please let me know.

Some other recommendations I got included the following, but of the  
ones we checked into it wasn't obvious that they'll do what we wanted.

FAMOZ
http://www.pierroton.inra.fr/genetics/labo/Software/Famoz/famozinstall/famozinstall_ct.html

Famsphere
http://webs.uvigo.es/acraaj/famsphere.htm

GIMLET
http://pbil.univ-lyon1.fr/software/Gimlet/gimlet%20frame1.html
Valiere, 2002 Mol. Ecol. Notes

KINGROUP www.kingroup.com

Gerud (Jones et al. 2005) http://www.bio.tamu.edu/USERS/ajones/JonesLab.htm

use MLTR by Kermit Ritland to obtain the mother genotype (check on his website
for the free program). The father is not as simple unless you
do a paternity-type analysis (PATRI is a good one if you do
not know all the potential fathers).  If you know nothing about
the potential fathers there is nothing that I know about right
now.

-- 
Michael Blouin
Dept. Zoology, Oregon State University
Corvallis, OR 97331-2914
http://oregonstate.edu/~blouinm/
Tel: 541-737-2362
Fax: 541-737-0501

blouinm@science.oregonstate.edu