Dan Gusfield

Efficient algorithms for inferring evolutionary trees

In this paper, we examine two related problems of inferring the evolutionary history of n objects, either from present characters of the objects or from several partial estimates of their evolutionary history. The first problem is called the Phylogeny problem, and second is the Tree Compatibility problem. Both of these problems are central in algorithmic approaches to the study of evolution and in other problems of historical reconstruction. In this paper, we show that both of these problems can be solved by graph theoretic methods in linear time, which is time optimal, and which is a significant improvement over existing methods.

Partition-distance: A problem and class of perfect graphs arising in clustering

Partitioning of a set of elements into disjoint clusters is a fundamental problem that arises in many applications. Different methods produce different partitions, so it is useful to have a measure of the similarity, or distance, between two or more partitions. In this paper we examine one distance measure used in a clustering application in computational genetics. We show how to efficiently compute the distance, and how this defines a new class of perfect graphs.

Linear time algorithms for finding and representing all the tandem repeats in a string

A tandem repeat (or square) is a string αα, where α is a non-empty string. We present an O(|S|)-time algorithm that operates on the suffix tree T(S) for a string S, finding and marking the endpoint in T(S) of every tandem repeat that occurs in S. This decorated suffix tree implicitly represents all occurrences of tandem repeats in S, and can be used to efficiently solve many questions concerning tandem repeats and tandem arrays in S. This improves and generalizes several prior efforts to efficiently capture large subsets of tandem repeats.

Very simple methods for all pairs network flow analysis

A very simple algorithm for the classical problem of computing the maximum network flow value between every pair of nodes in an undirected, capacitated n node graph is presented; as in the well-known Gomory–Hu method, the method given here uses only

Parametric optimization of sequence alignment

n - 1

Three fast algorithms for four problems in stable marriage

maximum flow computations. Our algorithm is implemented by adding only five simple lines of code to any program that produces a minimum cut; a program to produce an equivalent flow tree, which is a compact representation of the flow values, is obtained by adding only three simple lines of code to any program producing a minimum cut. A very simple version of the Gomory–Hu cut tree method that finds one minimum cut for every pair of nodes is also derived, and it is shown that the seemingly fundamental operation of that method, node contraction, is not needed, nor must crossing cuts be avoided. As a result, this version of the Gomory–Hu method is implemented by adding less than ten simple lines of code to any program that produces a minimum cut. The algor...

A graph theoretic approach to statistical data security

Theoptimal alignment or theweighted minimum edit distance between two DNA or amino acid sequences for a given set of weights is computed by classical dynamic programming techniques, and is widely used in molecular biology. However, in DNA and amino acid sequences there is considerable disagreement about how to weight matches, mismatches, insertions/deletions (indels or spaces), and gaps.Parametric sequence alignment is the problem of computing the optimal-valued alignment between two sequences as afunction of variable weights for matches, mismatches, spaces, and gaps. The goal is to partition the parameter space into regions (which are necessarily convex) such that in each region one alignment is optimal throughout and such that the regions are maximal for this property. In this paper we are primarily concerned with the structure of this convex decomposition, and secondarily with the complexity of computing the decomposition. The most striking results are the following: For the special case where only matches, mismatches, and spaces are counted, and where spaces are counted throughout the alignment, we show that the decomposition is surprisingly simple: all regions are infinite; there are at most n2/3 regions; the lines that bound the regions are all of the form Β=c + (c + 0.5)α; and the entire decomposition can be found inO(knm) time, wherek is the actual number of regions, andn<m are the lengths of the two strings. These results were found while implementing a large software package for parametric sequence analysis, and in turn have led to faster algorithms for those tasks. A conference version of this paper first appeared in [10].

The Fine Structure of Galls in Phylogenetic Networks

The stable marriage problem is a well-known problem of matching n men to n women to achieve a certain type of “stability;” the

A fundamental decomposition theory for phylogenetic networks and incompatible characters

O(n^2 )

An efficient algorithm for the All Pairs Suffix-Prefix Problem

time Gale-Shapley [GS] algorithm for finding two particular, but extreme, stable marriages (out of a possibly exponential number of stable marriages) is also well known. In this paper we consider four problems concerned with finding information about the set of all stable marriages, and with finding stable marriages other than those obtained by the Gale-Shapley algorithm. In particular, we give an