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Register a new userComputing the blocks of a quasi-median graph
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Added by
Sven Herrmann
Publication date
2012
fields
Informatics Engineering
and research's language is
English
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Quasi-median graphs are a tool commonly used by evolutionary biologists to visualise the evolution of molecular sequences. As with any graph, a quasi-median graph can contain cut vertices, that is, vertices whose removal disconnect the graph. These vertices induce a decomposition of the graph into blocks, that is, maximal subgraphs which do not contain any cut vertices. Here we show that the special structure of quasi-median graphs can be used to compute their blocks without having to compute the whole graph. In particular we present an algorithm that, for a collection of $n$ aligned sequences of length $m$, can compute the blocks of the associated quasi-median graph together with the information required to correctly connect these blocks together in run time $mathcal O(n^2m^2)$, independent of the size of the sequence alphabet. Our primary motivation for presenting this algorithm is the fact that the quasi-median graph associated to a sequence alignment must contain all most parsimonious trees for the alignment, and therefore precomputing the blocks of the graph has the potential to help speed up any method for computing such trees.
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Komlos [Tiling Turan theorems, Combinatorica, 20,2 (2000), 203{218] determined the asymptotically optimal minimum degree condition for covering a given proportion of vertices of a host graph by vertex-disjoint copies of a fixed graph. We show that the minimum degree condition can be relaxed in the sense that we require only a given fraction of vertices to have the prescribed degree.
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