Haplotyping as perfect phylogeny: conceptual framework and efficient solutions
Proceedings of the sixth annual international conference on Computational biology
Journal of Computer and System Sciences - Special issue on bioinformatics II
A Concise Necessary and Sufficient Condition for the Existence of a Galled-Tree
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The Fine Structure of Galls in Phylogenetic Networks
INFORMS Journal on Computing
Discrete Applied Mathematics
Haplotype inference by pure Parsimony
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Algorithm for haplotype inferring via galled-tree networks with simple galls
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Algorithms for imperfect phylogeny haplotyping (IPPH) with a single homoplasy or recombination event
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
Phylogeny- and parsimony-based haplotype inference with constraints
Information and Computation
Hi-index | 0.00 |
The problem of determining haplotypes from genotypes has gained considerable prominence in the research community since the beginning of the HapMap project. Here the focus is on determining the sets of SNP values of individual chromosomes (haplotypes), since such information better captures the genetic causes of diseases. One of the main algorithmic tools for haplotyping is based on the assumption that the evolutionary history for the original haplotypes satisfies perfect phylogeny. The algorithm can be applied only on individual blocks of chromosomes, in which it is assumed that recombinations either do not happen or happen with small frequencies. However, exact determination of blocks is usually not possible. It would be desirable to develop a method for haplotyping which can account for recombinations, and thus can be applied on multiblock sections of chromosomes. A natural candidate for such a method is haplotyping via phylogenetic networks or their simplified version: galled-tree networks, which were introduced by Wang, Zhang, Zhang ([25]) to model recombinations. However, even haplotyping via galled-tree networks appears hard, as the algorithms exist only for very special cases: the galled-tree network has either a single gall ([23]) or only small galls with two mutations each ([8]). Building on our previous results ([6]) we show that, in general, haplotyping via galled-tree networks is NP-complete, and thus indeed hard.