Running head: A Reduction Algorithm for Hybridization (2009)
Magnus Bordewich, Simone Linz, Katherine St. John, Charles Semple
duesseldorf.de
Bordewich, Magnus, Gascuel, Olivier, Huber, Katharina, Moulton, Vincent
Many phylogenetic algorithms search the space of possible trees using topological rearrangements and some optimality criterion. FastME is such an approach that uses the {em balanced minimum evolution...
Bordewich, Magnus, Gascuel, Olivier, Huber, Katharina, Moulton, Vincent
Many phylogenetic algorithms search the space of possible trees using topological rearrangements and some optimality criterion. FastME is such an approach that uses the {em balanced minimum evolution...
Identifying X-Trees with Few Characters (2008)
Magnus Bordewich, Charles Semple, Mike Steel
Previous work has shown the perhaps surprising result that, for any binary phylogenetic tree T, there is a set of four characters that define T. Here we deal with the general case, where T is an...
COMPUTING THE MINIMUM NUMBER OF HYBRIDIZATION EVENTS FOR A CONSISTENT EVOLUTIONARY HISTORY (2008)
Magnus Bordewich, Charles Semple
Abstract. It is now well-documented that the structure of evolutionary relationships between a set of present-day species is not necessarily tree-like. The reason for this is that reticulation events...
Stopping Times, Metrics and Approximate Counting (2008)
Magnus Bordewich, Marek Karpinski
Abstract. In this paper we examine the importance of the choice of metric in path coupling, and its relationship to stopping time analysis. We give strong evidence that stopping time analysis is no...
Identifying X-Trees with Few Characters (2008)
Magnus Bordewich, Charles Semple, Mike Steel
Previous work has shown the perhaps surprising result that, for any binary phylogenetic tree T, there is a set of four characters that define T. Here we deal with the general case, where T is an...
Selecting Taxa to Save or Sequence: Desirable Criteria and a Greedy Solution (2008)
Bordewich, Magnus, Rodrigo, Allen G., Semple, Charles
Three desirable properties for any method of selecting a subset of evolutionary units (EUs) for conservation or for genomic sequencing are discussed. These properties are spread, stability, and...
A Reduction Algorithm for Computing The Hybridization Number of Two Trees (2007)
Magnus Bordewich, Simone Linz, Katherine St. John, Charles Semple
Hybridization is an important evolutionary process for many groups of species. Thus, conflicting signals in a data set may not be the result of sampling or modeling errors, but due to the fact that...
Metric Construction, Stopping Times and Path Coupling (2005)
Bordewich, Magnus, Dyer, Martin, Karpinski, Marek
In this paper we examine the importance of the choice of metric in path coupling, and the relationship of this to \emph{stopping time analysis}. We give strong evidence that stopping time analysis is...
Bordewich, Magnus, Dyer, Martin, Karpinski, Marek
We give a new method for analysing the mixing time of a Markov chain using path coupling with stopping times. We apply this approach to two hypergraph problems. We show that the Glauber dynamics for...
C.: Identifying phylogenetic trees (2005)
Magnus Bordewich, Katharina T. Huber, Charles Semple
Abstract. A central problem that arises in evolutionary biology is that of displaying partitions of subsets of a finite set X on a tree whose vertices are partially labelled with the elements of X....
Path coupling using stopping times (2005)
Magnus Bordewich, Marek Karpinski
Abstract. We analyse the mixing time of Markov chains using path coupling with stopping times. We apply this approach to two hypergraph problems. We show that the Glauber dynamics for independent...
Magnus Bordewich, Martin Dyer, Marek Karpinski
Abstract We give a new method for analysing the mixing time of a Markov chain using path couplingwith stopping times. We apply this approach to two hypergraph problems. We show that the Glauber...
Magnus Bordewich, Martin Dyer, Marek Karpinski
We give a new method for analysing the mixing time of a Markov chain using path coupling with stopping times. We apply this approach to two hypergraph problems. We show that the Glauber dynamics for...
The Complexity of Counting and Randomised Approximation (2003)
In this thesis we examine the complexity of counting, both exactly and approx-imately. We first consider counting functions in phylogenetics, and prove some intractability results. The main result in...
The Tutte polynomial T (G; x, y) of a graph evaluates to many interesting combinatorial quantities at various points in the (x, y) plane, including the number of spanning trees, number of forests,...
A Reduction Algorithm for Computing The Hybridization Number of Two Trees
Bordewich, Magnus, Linz, Simone, St. John, Katherine, Semple, Charles
Hybridization is an important evolutionary process for many groups of species. Thus, conflicting signals in a data set may not be the result of sampling or modeling errors, but due to the fact that...