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A rearrangement operation makes a small graph-theoretical change to a phylogenetic network to transform it into another one. For unrooted phylogenetic trees and networks, popular rearrangement operations are tree bisection and reconnection…

Estimating phylogenetic trees, which depict the relationships between different species, from aligned sequence data (such as DNA, RNA, or proteins) is one of the main aims of evolutionary biology. However, tree reconstruction criteria like…

It has remained an open question for some time whether, given a set of not necessarily binary (i.e. "nonbinary") trees T on a set of taxa X, it is possible to determine in time f(r).poly(m) whether there exists a phylogenetic network that…

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 study the classical NP-hard problems of finding maximum-size subsets from given sets of $k$ terminal pairs that can be routed via edge-disjoint paths (MaxEDP) or node-disjoint paths (MaxNDP) in a given graph. The approximability of…

We study the problem of maximizing the number of full degree vertices in a spanning tree $T$ of a graph $G$; that is, the number of vertices whose degree in $T$ equals its degree in $G$. In cubic graphs, this problem is equivalent to…

Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…

It is a known fact that, given two rooted binary phylogenetic trees, the concept of maximum acyclic agreement forests is sufficient to compute hybridization networks with minimum hybridization number. In this work, we demonstrate by first…

Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…

Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…

We present an algorithm for computing a maximum agreement subtree of two unrooted evolutionary trees. It takes O(n^{1.5} log n) time for trees with unbounded degrees, matching the best known time complexity for the rooted case. Our…

Phylogenetic Diversity (PD) is a prominent quantitative measure of the biodiversity of a collection of present-day species (taxa). This measure is based on the evolutionary distance among the species in the collection. Loosely speaking, if…

Kloks, Kratsch, and Spinrad showed how treewidth and minimum-fill, NP-hard combinatorial optimization problems related to minimal triangulations, are broken into subproblems by block subgraphs defined by minimal separators. These ideas were…

Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…

Several computational problems in phylogenetic reconstruction can be formulated as restrictions of the following general problem: given a formula in conjunctive normal form where the literals are rooted triples, is there a rooted binary…

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…

A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…

We describe a method that will reconstruct an unrooted binary phylogenetic level-1 network on n taxa from the set of all quartets containing a certain fixed taxon, in O(n^3) time. We also present a more general method which can handle more…

Rooted triples, rooted binary phylogenetic trees on three leaves, are sufficient to encode rooted binary phylogenetic trees. That is, if $\mathcal T$ and $\mathcal T'$ are rooted binary phylogenetic $X$-trees that infers the same set of…

Phylogenetic networks are increasingly being considered as better suited to represent the complexity of the evolutionary relationships between species. One class of phylogenetic networks that has received a lot of attention recently is the…