Related papers: A note on convex characters, Fibonacci numbers and…

The Persistent Perfect phylogeny, also known as Dollo-1, has been introduced as a generalization of the well-known perfect phylogenetic model for binary characters to deal with the potential loss of characters. The problem of deciding the…

We give an algorithm that for an input n-vertex graph G and integer k>0, in time 2^[O(k)]n either outputs that the treewidth of G is larger than k, or gives a tree decomposition of G of width at most 5k+4. This is the first algorithm…

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…

We prove a conjecture of W.~Hackbusch in a bigger generality than in our previous article. Here we consider Tensor Train (TT) model with an arbitrary number of leaves and a corresponding "almost binary tree" for Hierarchical Tucker (HT)…

We define a search problem on trees that closely captures the backtracking behavior of all current practical graph isomorphism algorithms. Given two trees with colored leaves, the goal is to find two leaves of matching color, one in each of…

In this short note we prove that, given two (not necessarily binary) rooted phylogenetic trees T_1, T_2 on the same set of taxa X, where |X|=n, the hybridization number of T_1 and T_2 can be computed in time O^{*}(2^n) i.e. O(2^{n}…

We construct an encoding of finite strings over a fixed finite alphabet as natural numbers, based on a block partition of the Fibonacci sequence. Each position in the string selects one Fibonacci number from a dedicated block, with unused…

A tree $T$ on $2^n$ vertices is called set-sequential if the elements in $V(T)\cup E(T)$ can be labeled with distinct nonzero $(n+1)$-dimensional $01$-vectors such that the vector labeling each edge is the component-wise sum modulo $2$ of…

The maximum parsimony phylogenetic tree reconstruction problem is NP-hard, presenting a computational bottleneck for classical computing and motivating the exploration of emerging paradigms like quantum computing. To this end, we design…

We continue the study of $(\mathrm{tw},\omega)$-bounded graph classes, that is, hereditary graph classes in which the treewidth can only be large due to the presence of a large clique, with the goal of understanding the extent to which this…

Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a…

An $\alpha$-thin tree $T$ of a graph $G$ is a spanning tree such that every cut of $G$ has at most an $\alpha$ proportion of its edges in $T$. The Thin Tree Conjecture proposes that there exists a function $f$ such that for any $\alpha >…

Phylogenetic networks are directed acyclic graphs that depict the genomic evolution of related taxa. Reticulation nodes in such networks (nodes with more than one parent) represent reticulate evolutionary events, such as recombination,…

The kTree problem is a special case of Subgraph Isomorphism where the pattern graph is a tree, that is, the input is an $n$-node graph $G$ and a $k$-node tree $T$, and the goal is to determine whether $G$ has a subgraph isomorphic to $T$.…

The tree-cut width of a graph is a graph parameter defined by Wollan [J. Comb. Theory, Ser. B, 110:47-66, 2015] with the help of tree-cut decompositions. In certain cases, tree-cut width appears to be more adequate than treewidth as an…

In this paper we investigate mathematical questions concerning the reliability (reconstruction accuracy) of Fitch's maximum parsimony algorithm for reconstructing the ancestral state given a phylogenetic tree and a character. In particular,…

Statistically consistent estimation of phylogenetic trees or gene trees is possible if pairwise sequence dissimilarities can be converted to a set of distances that are proportional to the true evolutionary distances. Susko et al. (2004)…

Over the past decade, we witness an increasing amount of interest in the design of exact exponential-time and parameterized algorithms for problems in Graph Drawing. Unfortunately, we still lack knowledge of general methods to develop such…

Given an edge-weighted tree $T$ with $n$ leaves, sample the leaves uniformly at random without replacement and let $W_k$, $2 \le k \le n$, be the length of the subtree spanned by the first $k$ leaves. We consider the question, "Can $T$ be…

In molecular systematics, evolutionary trees are reconstructed from sequences at the tips under simple models of site substitution. A central question is how much sequence data is required to reconstruct a tree accurately? The answer…