Related papers: Testing the Agreement of Trees with Internal Label…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
An out-tree $T$ is an oriented tree with only one vertex of in-degree zero. A vertex $x$ of $T$ is internal if its out-degree is positive. We design randomized and deterministic algorithms for deciding whether an input digraph contains a…
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…
Different sources of information might tell different stories about the evolutionary history of a given set of species. This leads to (rooted) phylogenetic trees that "disagree" on triples of species, which we call "conflict triples". An…
Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…
Consider any locally checkable labeling problem $\Pi$ in rooted regular trees: there is a finite set of labels $\Sigma$, and for each label $x \in \Sigma$ we specify what are permitted label combinations of the children for an internal node…
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…
The tree inclusion problem is, given two node-labeled trees $P$ and $T$ (the ``pattern tree'' and the ``target tree''), to locate every minimal subtree in $T$ (if any) that can be obtained by applying a sequence of node insertion operations…
Labeling schemes seek to assign a short label to each node in a network, so that a function on two nodes can be computed by examining their labels alone. For the particular case of trees, optimal bounds (up to low order terms) were recently…
In this paper, we are interested in the number of red nodes in red-black trees. We first present an $O(n^2\log n)$ time dynamic programming solution for computing $r(n)$, the largest number of red internal nodes in a red-black tree on $n$…
This paper presents two new deterministic algorithms for constructing consensus trees. Given an input of k phylogenetic trees with identical leaf label sets and n leaves each, the first algorithm constructs the majority rule (+) consensus…
A multi-labeled tree, or MUL-tree, is a phylogenetic tree where two or more leaves share a label, e.g., a species name. A MUL-tree can imply multiple conflicting phylogenetic relationships for the same set of taxa, but can also contain…
We consider the well-studied pattern counting problem: given a permutation $\pi \in \mathbb{S}_n$ and an integer $k > 1$, count the number of order-isomorphic occurrences of every pattern $\tau \in \mathbb{S}_k$ in $\pi$. Our first result…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
We consider the tree consensus problem, an important problem in bioinformatics. Given a rooted tree $t$ and another tree $T$, one would like to incorporate compatible information from $T$ to $t$. This problem is a subproblem in the tree…
Given a set of leaf-labeled trees with identical leaf sets, the well-known "Maximum Agreement SubTree" problem (MAST) consists of finding a subtree homeomorphically included in all input trees and with the largest number of leaves. Its…
We give a short proof of Cayley's tree formula for counting the number of different labeled trees on $n$ vertices. The following nonlinear recursive relation for the number of labeled trees on $n$ vertices is deduced from a combinatorial…
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…
Agreement forests continue to play a central role in the comparison of phylogenetic trees since their introduction more than 25 years ago. More specifically, they are used to characterise several distances that are based on tree…
The input to the token swapping problem is a graph with vertices $v_1, v_2, \ldots, v_n$, and $n$ tokens with labels $1, 2, \ldots, n$, one on each vertex. The goal is to get token $i$ to vertex $v_i$ for all $i= 1, \ldots, n$ using a…