Related papers: On symmetries in phylogenetic trees
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 provide a short combinatorial proof of Cayley's formula by means of a bijective map to an outcome space of an urn-drawing problem. Furthermore we introduce an algebraic structure on the set of labeled trees, which provides a more…
A tanglegram consists of two binary rooted trees with the same number of leaves and a perfect matching between the leaves of the trees. We show that the two halves of a random tanglegram essentially look like two independently chosen random…
We give a short and direct proof of a remarkable identity that arises in the enumeration of labeled trees with respect to their indegree sequence, where all edges are oriented from the vertex with lower label towards the vertex with higher…
A normal network is uniquely determined by the set of phylogenetic trees that it displays. Given a set $\mathcal{P}$ of rooted binary phylogenetic trees, this paper presents a polynomial-time algorithm that reconstructs the unique binary…
Many discrete mathematics problems in phylogenetics are defined in terms of the relative labeling of pairs of leaf-labeled trees. These relative labelings are naturally formalized as tanglegrams, which have previously been an object of…
We apply the theory of markov random fields on trees to derive a phase transition in the number of samples needed in order to reconstruct phylogenies. We consider the Cavender-Farris-Neyman model of evolution on trees, where all the inner…
Given a permutation $\sigma$, its corresponding binary search tree is obtained by recursively inserting the values $\sigma(1),\ldots,\sigma(n)$ into a binary tree so that the label of each node is larger than the labels of its left subtree…
Consider any locally checkable labeling problem $\Pi$ in rooted regular trees: there is a finite set of labels $\Sigma$, and for each label $x \in \Sigma$ we specify what are permitted label combinations of the children for an internal node…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
A closed-form formula is derived for the number of occurrences of matches of a multiset of patterns among all ordered (plane-planted) trees with a given number of edges. A pattern looks like a tree, with internal nodes and leaves, but also…
Graham and Sloane proposed in 1980 a conjecture stating that every tree has a harmonious labelling, a graph labelling closely related to additive base. Very limited results on this conjecture are known. In this paper, we proposed a…
We prove that the multiplicity of a fixed eigenvalue $\alpha$ in a random recursive tree on $n$ vertices satisfies a central limit theorem with mean and variance asymptotically equal to $\mu_{\alpha} n$ and $\sigma^2_{\alpha} n$…
We introduce a non-increasing tree growth process $((T_n,\sigma_n),\, n\ge 1)$, where $T_n$ is a rooted labeled tree on $n$ vertices and ${\sigma}_n$ is a permutation of the vertex labels. The construction of $(T_{n},{\sigma}_n)$ from…
A tanglegram consists of two rooted binary trees and a perfect matching between their leaves, and a planar tanglegram is one that admits a layout with no crossings. We show that the problem of generating planar tanglegrams uniformly at…
One of the major outstanding conjectures in the study of chromatic symmetric functions (CSF's) states that trees are uniquely determined by their CSF's. Though verified on graphs of order up to twenty-nine, this result has been proved only…
Any Boolean function corresponds with a complete full binary decision tree. This tree can in turn be represented in a maximally compact form as a direct acyclic graph where common subtrees are factored and shared, keeping only one copy of…
We introduce regenerative tree growth processes as consistent families of random trees with n labelled leaves, n>=1, with a regenerative property at branch points. This framework includes growth processes for exchangeably labelled Markov…
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…
Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…