Related papers: On the Extremal Maximum Agreement Subtree Problem
The Maximum Agreement Forest problem has been extensively studied in phylogenetics. Most previous work is on two binary phylogenetic trees. In this paper, we study a generalized version of the problem: the Maximum Agreement Forest problem…
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…
Consider a set of labels $L$ and a set of trees ${\mathcal T} = \{{\mathcal T}^{(1), {\mathcal T}^{(2), ..., {\mathcal T}^{(k) \$ where each tree ${\mathcal T}^{(i)$ is distinctly leaf-labeled by some subset of $L$. One fundamental problem…
We present new and improved fixed-parameter algorithms for computing maximum agreement forests (MAFs) of pairs of rooted binary phylogenetic trees. The size of such a forest for two trees corresponds to their subtree prune-and-regraft…
Over some types of trees with a given number of vertices, which trees minimize or maximize the total number of subtrees or leaf containing subtrees are studied. Here are some of the main results:\ (1)\, Sharp upper bound on the total number…
Phylogenetic trees are leaf-labelled trees, where the leaves correspond to extant species (taxa), and the internal vertices represent ancestral species. The evolutionary history of a set of species can be explained by more than one…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of…
We determine upper and lower bounds for the number of maximum matchings (i.e., matchings of maximum cardinality) $m(T)$ of a tree $T$ of given order. While the trees that attain the lower bound are easily characterised, the trees with…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
We present efficient algorithms for computing a maximum agreement forest (MAF) of a pair of multifurcating (nonbinary) rooted trees. Our algorithms match the running times of the currently best algorithms for the binary case. The size of an…
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…
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 characterize the extremal trees that maximize the number of almost-perfect matchings, which are matchings covering all but one or two vertices, and those that maximize the number of strong almost-perfect matchings, which are matchings…
Consider a rooted tree $T$ with leaf-set $[n]$, and with all non-leaf vertices having out-degree $2$, at least. A rooted tree $\mathcal T$ with leaf-set $S\subset [n]$ is induced by $S$ in $T$ if $\mathcal T$ is the lowest common ancestor…
The {\sc Directed Maximum Leaf Out-Branching} problem is to find an out-branching (i.e. a rooted oriented spanning tree) in a given digraph with the maximum number of leaves. In this paper, we improve known parameterized algorithms and…
Evolutionary scenarios displaying reticulation events are often represented by rooted phylogenetic networks. Due to biological reasons, those events occur very rarely, and, thus, networks containing a minimum number of such events,…
Given two rooted phylogenetic trees on the same set of taxa X, the Maximum Agreement Forest problem (MAF) asks to find a forest that is, in a certain sense, common to both trees and has a minimum number of components. The Maximum Acyclic…
We give a 2-approximation algorithm for the Maximum Agreement Forest problem on two rooted binary trees. This NP-hard problem has been studied extensively in the past two decades, since it can be used to compute the Subtree…
Given a set of points in the Euclidean plane, the Euclidean \textit{$\delta$-minimum spanning tree} ($\delta$-MST) problem is the problem of finding a spanning tree with maximum degree no more than $\delta$ for the set of points such the…