Related papers: Reconstructing fully-resolved trees from triplet c…
We consider special cases of the two tree degree sequences problem. We show that if two tree degree sequences do not have common leaves then they always have edge-disjoint caterpillar realizations. By using a probabilistic method, we prove…
Suppose $G$ is a tree. Graham's "Tree Reconstruction Conjecture" states that $G$ is uniquely determined by the integer sequence $|G|$, $|L(G)|$, $|L(L(G))|$, $|L(L(L(G)))|$, $\ldots$, where $L(H)$ denotes the line graph of the graph $H$.…
We study distorted metrics on binary trees in the context of phylogenetic reconstruction. Given a binary tree $T$ on $n$ leaves with a path metric $d$, consider the pairwise distances $\{d(u,v)\}$ between leaves. It is well known that these…
A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…
We prove several hardness results on folding origami crease patterns. Flat-folding finite crease patterns is fixed-parameter tractable in the ply of the folded pattern (how many layers overlap at any point) and the treewidth of an…
This paper addresses the problem of finding a representation of a subtree distance, which is an extension of the tree metric. We show that a minimal representation is uniquely determined by a given subtree distance, and give a linear time…
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…
Poly-trees are singly connected causal networks in which variables may arise from multiple causes. This paper develops a method of recovering ply-trees from empirically measured probability distributions of pairs of variables. The method…
We describe a kernel of size 9k-8 for the NP-hard problem of computing the Tree Bisection and Reconnect (TBR) distance k between two unrooted binary phylogenetic trees. We achieve this by extending the existing portfolio of reduction rules…
We define, analyze, and give efficient algorithms for two kinds of distance measures for rooted and unrooted phylogenies. For rooted trees, our measures are based on the topologies the input trees induce on triplets; that is, on…
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…
We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct…
The evolution of aligned DNA sequence sites is generally modeled by a Markov process operating along the edges of a phylogenetic tree. It is well known that the probability distribution on the site patterns at the tips of the tree…
We prove that every tree of maximum degree $\Delta$ with $\ell$ leaves contains paths between leaves of at least $\log_{\Delta-1}((\Delta-2)\ell)$ distinct lengths. This settles in a strong form a conjecture of Narins, Pokrovskiy and…
Given a distance matrix consisting of pairwise distances between species, a distance-based phylogenetic reconstruction method returns a tree metric or equidistant tree metric (ultrametric) that best fits the data. We investigate…
We prove that, if $m$ is sufficiently large, every graph on $m+1$ vertices that has a universal vertex and minimum degree at least $\lfloor \frac{2m}{3} \rfloor$ contains each tree $T$ with $m$ edges as a subgraph. Our result confirms, for…
We consider the following graph reconstruction problem: given an unweighted connected graph $G = (V,E)$ with visible vertex set $V$ and an oracle which takes two vertices $u,v \in V$ and returns the shortest path distance between $u$ and…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
In this paper, we consider the problem of reconstructing trees from traces in the tree edit distance model. Previous work by Davies et al. (2019) analyzed special cases of reconstructing labeled trees. In this work, we significantly expand…
We study the problem of learning a node-labeled tree given independent traces from an appropriately defined deletion channel. This problem, tree trace reconstruction, generalizes string trace reconstruction, which corresponds to the tree…