Related papers: On the quartet distance given partial information
Ranked tree-child networks are a recently introduced class of rooted phylogenetic networks in which the evolutionary events represented by the network are ordered so as to respect the flow of time. This class includes the well-studied…
Inference of phylogenetic networks is of increasing interest in the genomic era. However, the extent to which phylogenetic networks are identifiable from various types of data remains poorly understood, despite its crucial role in…
We study the number of distance queries needed to identify certain properties of a hidden tree $T$ on $n$ vertices. A distance query consists of two vertices $x,y$, and the answer is the distance of $x$ and $y$ in $T$. We determine the…
Information distance can be defined not only between two strings but also in a finite multiset of strings of cardinality greater than two. We give an elementary proof for expressing the information distance in terms of plain Kolmogorov…
The last decade brought a significant increase in the amount of data and a variety of new inference methods for reconstructing the detailed evolutionary history of various cancers. This brings the need of designing efficient procedures for…
We propose the following conjecture: For every fixed $\alpha\in [0,\frac 13)$, each graph of minimum degree at least $(1+\alpha)\frac k2$ and maximum degree at least $2(1-\alpha)k$ contains each tree with $k$ edges as a subgraph. Our main…
In 2001 Allen and Steel showed that, if subtree and chain reduction rules have been applied to two unrooted phylogenetic trees, the reduced trees will have at most 28k taxa where k is the TBR (Tree Bisection and Reconnection) distance…
Rare events have played an increasing role in molecular phylogenetics as potentially homoplasy-poor characters.In this contribution we analyze the phylogenetic information content from a combinatorial point of view by consid-ering the…
We propose a consistent approach to the statistics of the shortest paths in random graphs with a given degree distribution. This approach goes further than a usual tree ansatz and rigorously accounts for loops in a network. We calculate the…
We consider the numerical taxonomy problem of fitting a positive distance function ${D:{S\choose 2}\rightarrow \mathbb R_{>0}}$ by a tree metric. We want a tree $T$ with positive edge weights and including $S$ among the vertices so that…
A cactus is a connected graph in which any two cycles have at most one common vertex. We determine the unique graph that maximizes the distance spectral radius over all cacti with fixed numbers of vertices and cycles, and thus prove a…
Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
Background: The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly…
Phylogenetic trees and networks are graphs used to model evolutionary relationships, with trees representing strictly branching histories and networks allowing for events in which lineages merge, called reticulation events. While the…
A Yule tree is the result of a branching process with constant birth and death rates. Such a process serves as an instructive null model of many empirical systems, for instance, the evolution of species leading to a phylogenetic tree.…
An added edge to a graph is called an inset edge. Predicting k inset edges which minimize the average distance of a graph is known to be NP-Hard. When k = 1 the complexity of the problem is polynomial. In this paper, we further find the…
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…
The information rate for an access structure is the reciprocal of the load of the optimal secret sharing scheme for this structure. We determine this value for all trees: it is 1/(2-1/c), where c is the size of the largest core of the tree.…
Rotation distances measure the differences in structure between rooted ordered binary trees. The one-dimensional skeleta of associahedra are rotation graphs, where two vertices representing trees are connected by an edge if they differ by a…