Paul E. Kearney

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MOTIVATION Traditional sequence distances require an alignment and therefore are not directly applicable to the problem of whole genome phylogeny where events such as rearrangements make full length alignments impossible. We present a sequence distance that works on unaligned sequences using the information theoretical concept of Kolmogorov complexity and a(More)
This paper presents the MESSAGE/UML agent oriented software engineering methodology and illustrates it on an analysis case study. The methodology covers MAS analysis and design and is intended for use in mainstream software engineering departments. MESSAGE integrates into a coherent AOSE methodology some basic agent related concepts such as organisation,(More)
A critical step in all quartet methods for constructing evolutionary trees is the inference of the topology for each set of four sequences (i.e. quartet). It is a well–known fact that all quartet topology inference methods make mistakes that result in the incorrect inference of quartet topology. These mistakes are called quartet errors. In this paper, two(More)
The comparison of evolutionary trees is a fundamental problem in evolutionary biology. Different evolutionary hypotheses (or conflicting phylogenies) arise when different phylogenetic reconstruction methods are applied to the same data set, or when a single method is applied to different data sets (e.g. different genes). Several similarity metrics between(More)
Inferring evolutionary trees has long been a challenging problem both for biologists and computer scientists. In recent years research has concentrated on the quartet method paradigm for inferring evolutionary trees. Quartet methods proceed by rst inferring the evolutionary history for every set of four species (resulting in a set Q of inferred quartet(More)
Given a graph G = (V; E) and a positive integer k, the Phylogenetic k-Root Problem asks for a (unrooted) tree T without degree-2 nodes such that its leaves are labeled by V and (u; v) 2 E if and only if dT (u; v) k. If the vertices in V are also allowed to be internal nodes in T , then we have the Steiner k-Root Problem. Moreover, if a particular subset S(More)
We present the first polynomial algorithm for recognizing tree powers. A graph G is a tree power if there is a tree T and a positive integer k such that T k ( G, k Ž . where x and y are adjacent in T if and only if d x, y F k. We also show that a T natural extension of tree power recognition is NP-complete, namely, given a graph G and a positive integer r,(More)
It is now routine for biologists to conduct evolutionary analyses of large DNA and protein sequence datasets. A computational bott leneck in these analyses is the recovery" of the topology of the evolutionary tree for a set of sequences. This paper presents a practical solution to this challenging problem. In particular, a new technique, called(More)