Related papers: Computing a Relevant Set of Nonbinary Maximum Acyc…
We present a simple 4-approximation algorithm for computing a maximum agreement forest of multiple unrooted binary trees. This algorithm applies LP rounding to an extension of a recent ILP formulation of the maximum agreement forest problem…
Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic…
It has recently been shown that the NP-hard problem of calculating the minimum number of hybridization events that is needed to explain a set of rooted binary phylogenetic trees by means of a hybridization network is fixed-parameter…
Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…
Rooted phylogenetic networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some well-defined sense simultaneously represents them all. We review these four models and investigate…
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is only concerned with the comparison of labeled trees of two…
The maximum parsimony phylogenetic tree reconstruction problem is NP-hard, presenting a computational bottleneck for classical computing and motivating the exploration of emerging paradigms like quantum computing. To this end, we design…
A binary phylogenetic network on a taxon set $X$ is a rooted acyclic digraph in which the degree of each nonleaf node is three and its leaves (i.e.degree-one nodes) are uniquely labeled with the taxa of $X$. It is tree-child if each nonleaf…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…
Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…
Throughout the last decade, we have seen much progress towards characterising and computing the minimum hybridisation number for a set P of rooted phylogenetic trees. Roughly speaking, this minimum quantifies the number of hybridisation…
Most research on query optimization has centered on binary join algorithms like hash join and sort-merge join. However, recent years have seen growing interest in theoretically optimal algorithms, notably Yannakakis' algorithm. These…
Phylogenetic trees describe the relationships between species in the evolutionary process, and provide information about the rates of diversification. To understand the mechanisms behind macroevolution, we consider a class of multitype…
Phylogenetic trees are frequently used to model evolution. Such trees are typically reconstructed from data like DNA, RNA, or protein alignments using methods based on criteria like maximum parsimony (amongst others). Maximum parsimony has…
We analyse a maximum-likelihood approach for combining phylogenetic trees into a larger `supertree'. This is based on a simple exponential model of phylogenetic error, which ensures that ML supertrees have a simple combinatorial description…
Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
The supertree construction problem is about combining several phylogenetic trees with possibly conflicting information into a single tree that has all the leaves of the source trees as its leaves and the relationships between the leaves are…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…