Related papers: On the enumeration of leaf-labelled increasing tre…
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…
Weighted recursive trees are built by adding successively vertices with predetermined weights to a tree: each new vertex is attached to a parent chosen at random with probability proportional to its weight. In the case where the total…
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…
A new tree model is introduced based on ordered trees, by distinguishing exactly one child of each node that \emph{has} children. The basic enumeration leads to a cubic equation of the generating function. The extraction of its coefficients…
Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…
Recently proposed budding tree is a decision tree algorithm in which every node is part internal node and part leaf. This allows representing every decision tree in a continuous parameter space, and therefore a budding tree can be jointly…
In this paper we investigate an extremal problem on binary phylogenetic trees. Given two such trees $T_1$ and $T_2$, both with leaf-set ${1,2,...,n}$, we are interested in the size of the largest subset $S \subseteq {1,2,...,n}$ of leaves…
We discuss a notion of convergence for binary trees that is based on subtree sizes. In analogy to recent developments in the theory of graphs, posets and permutations we investigate some general aspects of the topology, such as a…
We consider uniform random permutations drawn from a family enumerated through generating trees. We develop a new general technique to establish a central limit theorem for the number of consecutive occurrences of a fixed pattern in such…
Billey et al. [arXiv:1507.04976] have recently discovered a surprisingly simple formula for the number $a_n(\sigma)$ of leaf-labelled rooted non-embedded binary trees (also known as phylogenetic trees) with $n\geq 1$ leaves, fixed (for the…
Measures of tree balance play an important role in different research areas such as mathematical phylogenetics or theoretical computer science. The balance of a tree is usually quantified in a single number, called a balance or imbalance…
We investigate the statistics of trees grown from some initial tree by attaching links to preexisting vertices, with attachment probabilities depending only on the valence of these vertices. We consider the asymptotic mass distribution that…
In this paper we investigate the geometry of a discrete Bayesian network whose graph is a tree all of whose variables are binary and the only observed variables are those labeling its leaves. We provide the full geometric description of…
We consider the problem of computing the measure of a regular set of infinite binary trees. While the general case remains unsolved, we show that the measure of a language can be computed when the set is given in one of the following three…
We define a new balance index for rooted phylogenetic trees based on the symmetry of the evolutive history of every set of 4 leaves. This index makes sense for multifurcating trees and it can be computed in time linear in the number of…
In mathematical phylogenetics, labeled histories describe the sequences by which sets of labeled lineages coalesce to a shared ancestral lineage. We study labeled histories for at-most-$r$-furcating trees. Consider a rooted leaf-labeled…
We study the problem of enumerating Braess edges for Kemeny's constant in trees. We obtain bounds and asympotic results for the number of Braess edges in some families of trees.
For a pair consisting of a gene tree and a species tree, the ancestral configurations at an internal node of the species tree are the distinct sets of gene lineages that can be present at that node. Ancestral configurations appear in…
A relaxed $k$-ary tree is an ordered directed acyclic graph with a unique source and sink in which every node has out-degree $k$. These objects arise in the compression of trees in which some repeated subtrees are factored and repeated…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…