Related papers: On the quartet distance given partial information
Let $k$, $d$ be a positive integer, $G$ be a connected graph of order $n$, $T$ be a tree. The leaf distance of a tree is defined as the minimum distance between any two leaves. For $v\in V(T)$, the leaf degree of $v$ in $T$ is the number of…
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…
Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we…
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…
It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees,…
In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…
The number of the non-shared edges of two phylogenies is a basic measure of the dissimilarity between the phylogenies. The non-shared edges are also the building block for approximating a more sophisticated metric called the nearest…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
Terraces are potentially large sets of trees with precisely the same likelihood or parsimony score, which can be induced by missing sequences in partitioned multi-locus phylogenetic data matrices. The set of trees on a terrace can be…
We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have…
We prove that for any pair of constants $\epsilon>0$ and $\Delta$ and for $n$ sufficiently large, every family of trees of orders at most $n$, maximum degrees at most $\Delta$, and with at most $\binom{n}{2}$ edges in total packs into…
Luo, Tian and Wu conjectured in 2022 that for any tree $T$ with bipartition $X$ and $Y$, every $k$-connected bipartite graph $G$ with $\delta(G) \geq k + t$, where $t = \max\{|X|,|Y |\}$, contains a subtree $T' \cong T$ such that $G-V(T')$…
A conjecture of Luo, Tian and Wu (2022) says that for every positive integer $k$ and every finite tree $T$ with bipartition $X$ and $Y$ (denote $t = \max\{|X|,|Y |\})$, every $k$-connected bipartite graph $G$ with $\delta(G) \geq k + t$…
We compute a number of distance-dependent universal scaling functions characterizing the distance statistics of large maps of genus one. In particular, we obtain explicitly the probability distribution for the length of the shortest…
Over the past few years, insights from computer science, statistical physics, and information theory have revealed phase transitions in a wide array of high-dimensional statistical problems at two distinct thresholds: One is the…
Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…
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…
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…
Phylogenetic inference-the derivation of a hypothesis for the common evolutionary history of a group of species- is an active area of research at the intersection of biology, computer science, mathematics, and statistics. One assumes the…
In a recent paper on 'Estimating Species Trees from Unrooted Gene Trees' Liu and Yu observe that the distance matrix on the underlying taxon set, which is built up from expected internode distances on gene trees under the multispecies…