11 citations · 23 across the 30 of their papers we have counts for
17 papers · 1 filter
SPRINT: A fast, new software tool for reconstructing the evolutionary past of polyploid datasets
Liam J. Maher, Taoyang Wu, Katharina T. Huber
Polyploidization is an important evolutionary process which affects organisms ranging from plants to fish and fungi. The signal left behind by it is in the form of a species' ploid…
Planar Rooted Phylogenetic Networks
Vincent Moulton, Taoyang Wu
A rooted phylogenetic network is a directed acyclic graph with a single root, whose sinks correspond to a set of species. As such networks are useful for representing the evolution…
Encoding and ordering X-cactuses
Andrew Francis, Katharina T. Huber, Vincent Moulton +1
Phylogenetic networks are a generalization of evolutionary or phylogenetic trees that are commonly used to represent the evolution of species which cross with one another. A specia…
Quarnet inference rules for level-1 networks
Katharine T. Huber, Vincent Moulton, Charles Semple +1
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic…
UPGMA and the normalized equidistant minimum evolution problem
Vincent Moulton, Andreas Spillner, Taoyang Wu
UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is a widely used clustering method. Here we show that UPGMA is a greedy heuristic for the normalized equidistant minimum e…
A cubic-time algorithm for computing the trinet distance between level-1 networks
Vincent Moulton, James Oldman, Taoyang Wu
In evolutionary biology, phylogenetic networks are constructed to represent the evolution of species in which reticulate events are thought to have occurred, such as recombination…
Bounds for phylogenetic network space metrics
Andrew Francis, Katharina Huber, Vincent Moulton +1
Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was intr…
Binets: fundamental building blocks for phylogenetic networks
Leo van Iersel, Vincent Moulton, Eveline de Swart +1
Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Esse…
Transforming phylogenetic networks: Moving beyond tree space
Katharina T. Huber, Vincent Moulton, Taoyang Wu
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networ…
Reduction rules for the maximum parsimony distance on phylogenetic trees
Steven Kelk, Mareike Fischer, Vincent Moulton +1
In phylogenetics, distances are often used to measure the incongruence between a pair of phylogenetic trees that are reconstructed by different methods or using different regions o…
On joint subtree distributions under two evolutionary models
Taoyang Wu, Kwok Pui Choi
In population and evolutionary biology, hypotheses about micro-evolutionary and macro-evolutionary processes are commonly tested by comparing the shape indices of empirical evoluti…
Folding and unfolding phylogenetic trees and networks
Katharina T. Huber, Vincent Moulton, Mike Steel +1
Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic net…
Clades and clans: a comparison study of two evolutionary models
Sha Zhu, Cuong Than, Taoyang Wu
The Yule-Harding-Kingman (YHK) model and the proportional to distinguishable arrangements (PDA) model are two binary tree generating models that are widely used in evolutionary bio…
Reconstruction of Network Evolutionary History from Extant Network Topology and Duplication History
Si Li, Kwok Pui Choi, Taoyang Wu +1
Genome-wide protein-protein interaction (PPI) data are readily available thanks to recent breakthroughs in biotechnology. However, PPI networks of extant organisms are only snapsho…
On Patchworks and Hierarchies
Andreas Dress, Vincent Moulton, Mike Steel +1
Motivated by questions in biological classification, we discuss some elementary combinatorial and computational properties of certain set systems that generalize hierarchies, namel…
Reconciliation of Gene and Species Trees With Polytomies
Yu Zheng, Taoyang Wu, Louxin Zhang
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs)…
Species, Clusters and the 'Tree of Life': A graph-theoretic perspective
Andreas Dress, Vincent Moulton, Mike Steel +1
A hierarchical structure describing the inter-relationships of species has long been a fundamental concept in systematic biology, from Linnean classification through to the more re…