Related papers: The maximum agreement subtree problem

Given $d\geq 2$ and two rooted $d$-ary trees $D$ and $T$ such that $D$ has $k$ leaves, the density $\gamma(D,T)$ of $D$ in $T$ is the proportion of all $k$-element subsets of leaves of $T$ that induce a tree isomorphic to $D$, after erasing…

Rooted binary perfect phylogenies provide a generalization of rooted binary unlabeled trees in which each leaf is assigned a positive integer value that corresponds in a biological setting to the count of the number of indistinguishable…

Three standard subtree transfer operations for binary trees, used in particular for phylogenetic trees, are: tree bisection and reconnection ($TBR$), subtree prune and regraft ($SPR$) and rooted subtree prune and regraft ($rSPR$). For a…

We solve a class of optimization problems for (phylogenetic) $X$-trees or their shapes. These problems have recently appeared in different contexts, e.g. in the context of the impact of tree shapes on the size of TBR neighborhoods, but so…

A subtree of a tree is any induced subgraph that is again a tree (i.e., connected). The mean subtree order of a tree is the average number of vertices of its subtrees. This invariant was first analyzed in the 1980s by Jamison. An intriguing…

Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP).…

Binary rooted trees, both in the ordered and in the un-ordered case, are well studied structures in the field of combinatorics. The aim of this work is to study particular patterns in these classes of trees. We consider completely…

We give a 2-approximation algorithm for the Maximum Agreement Forest problem on two rooted binary trees. This NP-hard problem has been studied extensively in the past two decades, since it can be used to compute the Subtree…

Phylogenetic networks are a flexible model of evolution that can represent reticulate evolution and handle complex data. Tree-based networks, which are phylogenetic networks that have a spanning tree with the same root and leaf-set as the…

We consider NCA labeling schemes: given a rooted tree $T$, label the nodes of $T$ with binary strings such that, given the labels of any two nodes, one can determine, by looking only at the labels, the label of their nearest common…

A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…

We show that there exists a constant $c>0$ such that every $n$-vertex tree $T$ with $\Delta(T)\le cn$ has Ramsey number $R(T)=\max\{t_1+2t_2,2t_1\}-1$, where $t_1\ge t_2$ are the sizes of the bipartition classes of $T$. This improves an…

We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…

We study the size and structure of the largest common subtree (LCS) between two independent Bienaym\'e trees conditioned to have size $n$. When the trees are critical with finite $2$nd and $(2+\kappa)$th moment respectively for some…

The {\sc Directed Maximum Leaf Out-Branching} problem is to find an out-branching (i.e. a rooted oriented spanning tree) in a given digraph with the maximum number of leaves. In this paper, we improve known parameterized algorithms and…

The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…

Let $n\geq\nu$, let $T$ be an $n$-vertex tree with bipartition class sizes $t_1\geq t_2$, and let $S$ be a $\nu$-vertex tree with bipartition class sizes $\tau_1\geq\tau_2$. Using four natural constructions, we show that the Ramsey number…

We consider extremal problems related to decks and multidecks of rooted binary trees (a.k.a. rooted phylogenetic tree shapes). Here, the deck (resp. multideck) of a tree $T$ refers to the set (resp. multiset) of leaf induced binary subtrees…

Trees without vertices of degree $2$ are sometimes named topological trees. In this work, we bring forward the study of the inducibility of (rooted) topological trees with a given number of leaves. The inducibility of a topological tree $S$…

A binary tanglegram is a pair <S,T> of binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example in phylogenetics or software engineering, it is required…