Who is Who in Phylogenetic Networks

Publication no #2186   Type :   Html | Bib | Both

Created: 2012-03-20 13:56:50     Modified: 2013-01-04 23:24:32

2186 Bonnie Kirkpatrick, Yakir Reshef, Hilary Finucane, Haitao Jiang, Binhai Zhu and Richard M. Karp. Comparing Pedigree Graphs. In JCB, Vol. 19(9):998-1014, 2012. Keywords: distance between networks, from network, pedigree. Note: http://arxiv.org/abs/1009.0909, preliminary version as poster at WABI 2010.         Toggle abstract "Pedigree graphs, or family trees, are typically constructed by an expensive process of examining genealogical records to determine which pairs of individuals are parent and child. New methods to automate this process take as input genetic data from a set of extant individuals and reconstruct ancestral individuals. There is a great need to evaluate the quality of these methods by comparing the estimated pedigree to the true pedigree. In this article, we consider two main pedigree comparison problems. The first is the pedigree isomorphism problem, for which we present a linear-time algorithm for leaf-labeled pedigrees. The second is the pedigree edit distance problem, for which we present (1) several algorithms that are fast and exact in various special cases, and (2) a general, randomized heuristic algorithm. In the negative direction, we first prove that the pedigree isomorphism problem is as hard as the general graph isomorphism problem, and that the sub-pedigree isomorphism problem is NP-hard. We then show that the pedigree edit distance problem is APX-hard in general and NP-hard on leaf-labeled pedigrees. We use simulated pedigrees to compare our edit-distance algorithms to each other as well as to a branch-and-bound algorithm that always finds an optimal solution. © 2012, Mary Ann Liebert, Inc." @Article{KRFJZK2012,       AUTHOR = {Kirkpatrick, Bonnie and Reshef, Yakir and Finucane, Hilary and Jiang, Haitao and Zhu, Binhai and Karp, Richard M.},       TITLE = {Comparing Pedigree Graphs},       YEAR = {2012},       JOURNAL = {JCB},       VOLUME = {19},       NUMBER = {9},       PAGES = {998-1014},       URL = {http://dx.doi.org/10.1089/cmb.2011.0254},       NOTE = {http://arxiv.org/abs/1009.0909, preliminary version as poster at WABI 2010},       KEYWORDS = {distance between networks, from network, pedigree} }