Bielefeld University - AG Genome Informatics

Algorithms for parsimony and minimum perfect phylogeny haplotyping problems, Nov. 19th, 2007, Martin Milanic

I will present the paper by van Iersel, Keijsper, Kelk and Stougie: Shorelines of islands of tractability: Algorithms for parsimony and minimum perfect phylogeny haplotyping problems. This is the journal version of their WABI 2006 paper "Beaches of islands of tractability: Algorithms for parsimony and minimum perfect phylogeny haplotyping problems" and contains new approximation results for PH and MPPH not found in the WABI version. Both papers contain extensions of some results from the paper by Sharan, Halldorsson and Istrail,Islands of Tractability for Parsimony Haplotyping.

The paper by Sharan et al. is just for further reading; you don't have to read it for the Journal Club.

The paper by van Iersel et al. is written in purely "CS style" and is almost free of any biological discussion (slightly more of which can be found in the paper by Sharan et al.). There are several variants of haplotyping problems and their restrictions discussed in this paper. To keep track of them, you should definitely read the Introduction. You can safely skip the hardness results (Section II). I will focus the presentation on polynomial results (Section III). Especially interesting is subsection III.A (Parsimony Haplotyping, pages 9-12) with its graph-theoretic approach, where an efficient algorithm, based on the nice structure of a certain graph (the so-called "compatibility graph"), is given for a variant of the problem. Take a look also at the easy part of subsection III.B (pages 12-14), where two reductions from Minimum Perfect Phylogeny Haplotyping to Parsimony Haplotyping are described. I will conclude the presentation with an overview of the approximation results (Section IV), and the open questions.