A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks (2009)
Huber, Katharina T., Van Iersel, Leo, Kelk, Steven, Suchecki, Radoslaw
Recently much attention has been devoted to the construction of phylogenetic networks which generalize phylogenetic trees in order to accommodate complex evolutionary processes. Here we present an...
Inferring polyploid phylogenies from multiply-labeled gene trees (2009)
Lott, Martin, Spillner, Andreas, Huber, Katharina T, Petri, Anna, Oxelman, Bengt, Moulton, Vincent
Abstract Background Gene trees that arise in the context of reconstructing the evolutionary history of polyploid species are often multiply-labeled, that is, the same leaf label can occur several...
A Note on Encodings of Phylogenetic Networks of Bounded Level (2009)
Gambette, Philippe, Huber, Katharina T.
Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of...
PADRE: a package for analyzing and displaying reticulate evolution (2009)
Lott, Martin, Spillner, Andreas, Huber, Katharina T., Moulton, Vincent
Summary: Recent advances in gene sequencing for polyploid species, coupled with standard phylogenetic tree reconstruction, leads to gene trees in which the same species can label several leaves. Such...
Using supernetworks to distinguish hybridization from lineage-sorting (2008)
Holland, Barbara R, Benthin, Steffi, Lockhart, Peter J, Moulton, Vincent, Huber, Katharina T
Abstract Background A simple and widely used approach for detecting hybridization in phylogenies is to reconstruct gene trees from independent gene loci, and to look for gene tree incongruence....
REPLACING CLIQUES BY STARS IN QUASI-MEDIAN GRAPHS (2008)
Katharina T. Huber, Vincent Moulton, Charles Semple
Abstract. For a multi-set Σ of splits (bipartitions) of a finite set X, we introduce the multi-split graph G(Σ). This graph is a natural extension of the Buneman graph. Indeed, it is shown that...
Katharina T. Huber, Michael Langton, David Penny, Vincent Moulton, Michael Hendy
*To whom correspondence should be addressed.
Byrka, Jaroslaw, Gawrychowski, Pawel, Huber, Katharina T., Kelk, Steven
This article concerns the following question arising in computational evolutionary biology. For a given subclass of phylogenetic networks, what is the maximum value of 0 = 0.61. We note that all the...
Untangling Complex Histories of Genome Mergings in High Polyploids (2007)
Brysting, Anne K., Oxelman, Bengt, Huber, Katharina T., Moulton, Vincent, Brochmann, Christian
Polyploidy, the duplication of entire genomes, plays a major role in plant evolution. In allopolyploids, genome duplication is associated with hybridization between two or more divergent genomes....
Reconstructing the Evolutionary History of Polyploids From Multi-labelled Trees (2006)
Huber, Katharina T., Oxelman, Bengt, Lott, Martin, Moulton, Vincent
In recent studies, phylogenetic networks have been derived from so-called multi-labelled trees in order to understand the origins of certain polyploids. Although the trees used in these studies were...
Reconstructing the Evolutionary History of Polyploids from Multilabeled Trees (2006)
Huber, Katharina T., Oxelman, Bengt, Lott, Martin, Moulton, Vincent
In recent studies, phylogenetic networks have been derived from so-called multilabeled trees in order to understand the origins of certain polyploids. Although the trees used in these studies were...
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....
M.: Four characters suffice to convexly define a phylogenetic tree (2005)
Katharina T. Huber, Vincent Moulton, Mike Steel
Abstract. It was recently shown that just five characters (functions on a finite set X) suffice to convexly define a trivalent tree with leaf set X. Here we show that four characters suffice which,...
Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny (2004)
Holland, Barbara R., Huber, Katharina T., Moulton, Vincent, Lockhart, Peter J.
Building species phylogenies from genome data requires the evaluation of phylogenetic evidence from independent gene loci. We propose an approach to do this using consensus networks. We compare gene...
Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny (2004)
Holland, Barbara R., Huber, Katharina T., Moulton, Vincent, Lockhart, Peter J.
Building species phylogenies from genome data requires the evaluation of phylogenetic evidence from independent gene loci. We propose an approach to do this using consensus networks. We compare gene...
Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny (2004)
Holland, Barbara R., Huber, Katharina T., Moulton, Vincent, Lockhart, Peter J.
Building species phylogenies from genome data requires the evaluation of phylogenetic evidence from independent gene loci. We propose an approach to do this using consensus networks. We compare gene...