Parsimony haplotyping is the problem of finding a set of haplotypes of minimum cardinality that explains a given set of genotypes, where a genotype is explained by two haplotypes if it can be obtained as a combination of the two. This problem is NP-complete in the general case, but polynomially solvable for    $(k,l)$      -bounded instances for certain   $k$       and    $l$      . Here,   $k$       denotes the maximum number of ambiguous sites in any genotype, and   $l$       is the maximum number of genotypes that are ambiguous at the same site. Only the complexity of the    $(*,2)$      -bounded problem is still unknown, where   $*$       denotes no restriction. It has been proved that   $(*,2)$      -bounded instances have compatibility graphs that can be constructed from cliques and circuits by pasting along an edge. In this paper, we give a constructive proof of the fact that   $(*,2)$      -bounded instances are polynomially solvable if the compatibility graph is constructed by pasting cliques, trees and circuits along a bounded number of edges. We obtain this proof by solving a slightly generalized problem on circuits, trees and cliques respectively, and arguing that all possible combinations of optimal solutions for these graphs that are pasted along a bounded number of edges can be enumerated efficiently.
['Jcm Judith Keijsper', 'Tim Oosterwijk']
Tractable cases of (*,2)-bounded parsimony haplotyping