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We will present two methods for constructing suffix trees in detail, Ukkonen's method and Weiner's method. Weiner was the first to show that suffix trees can be built in linear time, and his method is presented both for its historical importance and for some different technical ideas that it contains. However, lJkkonen's method is equally fast and uses far(More)
The history and motivation Although I didn't know it at the time, I began writing this book in the summer of 1988 when I was part of a computer science research group at the Human Genome Center of Lawrence Berkeley Laboratory. Our group followed the standard assumption that biologically meaningful results could come from considering DNA as a one-dimensional(More)
A phylogenetic network is a generalization of a phylogenetic tree, allowing structural properties that are not tree-like. In a seminal paper, Wang et al.(1) studied the problem of constructing a phylogenetic network, allowing recombination between sequences, with the constraint that the resulting cycles must be disjoint. We call such a phylogenetic network(More)
A full haplotype map of the human genome will prove extremely valuable as it will be used in large-scale screens of populations to associate specific haplotypes with specific complex genetic-influenced diseases. A haplotype map project has been announced by NIH. The biological key to that project is the surprising fact that some human genomic DNA can be(More)
In an instance of size <italic>n</italic> of the stable marriage problem, each of <italic>n</italic> men and <italic>n</italic> women ranks the members of the opposite sex in order of preference. A stable matching is a complete matching of men and women such that no man and woman who are not partners both prefer each other to their actual partners under the(More)