Related papers: A bijection between phylogenetic trees and plane o…
We study the bounded regions in a generic slice of the hyperplane arrangement in $\mathbb{R}^n$ consisting of the hyperplanes defined by $x_i$ and $x_i+x_j$. The bounded regions are in bijection with several classes of combinatorial…
Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…
Motivated by the bijection between Schnyder labelings of a plane triangulation and partitions of its inner edges into three trees, we look for binary labelings for quadrangulations (whose edges can be partitioned into two trees). Our…
An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. Species here is a general denomination for biological species, spoken languages or any other…
A bijection is constructed between two sets of height restricted lattice paths by means of translating them in two tree classe, namely plane trees and Elena trees. An old bijection between them can be used now for that actual problem.
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
The number of tree-rooted maps, that is, rooted planar maps with a distinguished spanning tree, of size $n$ is C(n)C(n+1) where C(n)=binomial(2n,n)/(n+1) is the nth Catalan number. We present a (long awaited) simple bijection which explains…
A rooted phylogenetic network is a directed acyclic graph with a single root, whose sinks correspond to a set of species. As such networks are useful for representing the evolution of species that have undergone reticulate evolution, there…
We exploit a bijection between plane recursive trees and Stirling permutations; this yields the equivalence of some results previously proven separately by different methods for the two types of objects as well as some new results. We also…
An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of…
We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have…
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 study the set of NBC sets (no broken circuit sets) of the Linial arrangement and deduce a constructive bijection to the set of local binary search trees. We then generalize this construction to two families of Linial type arrangements…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
Rooted phylogenetic networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some well-defined sense simultaneously represents them all. We review these four models and investigate…
We construct a direct natural bijection between descending plane partitions without any special part and permutations. The directness is in the sense that the bijection avoids any reference to nonintersecting lattice paths. The advantage of…