Genome Halving with an Outgroup

Some genomes are known to have incurred a genome doubling (tetraploidization) event in their evolutionary history, and this is reflected today in patterns of duplicated segments scattered throughout their chromosomes. These duplications may be used as data to "halve" the genome, i.e. to reconstruct the an cestral genome at the moment of tetraploidization, but the solution is often highly non-unique. To resolve this problem, we adapt the genome halving algorithm of El-Mabrouk and Sankoff to take account of an external reference genome. We apply this to reconstruct the tetraploid ancestor of maize, using either rice or sorghum as the reference.