Related papers: A class of phylogenetic networks reconstructable f…

Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees,…

Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic…

Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use…

In the study of rooted phylogenetic networks, analyzing the set of rooted phylogenetic trees that are embedded in such a network is a recurring task. From an algorithmic viewpoint, this analysis almost always requires an exhaustive search…

Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…

The history of gene families -- which are equivalent to event-labeled gene trees -- can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes.…

Let $X$ be a finite set, $\mathcal N$ be a reticulation-visible network on $X$, and $\mathcal T$ be a rooted binary phylogenetic tree. We show that there is a polynomial-time algorithm for deciding whether or not $\mathcal N$ displays…

In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…

In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations…

Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…

A graph is a $k$-leaf power of a tree $T$ if its vertices are leaves of $T$ and two vertices are adjacent in $T$ if and only if their distance in $T$ is at most $k$. Then $T$ is a $k$-leaf root of $G$. This notion was introduced by…

We study the problem of learning a node-labeled tree given independent traces from an appropriately defined deletion channel. This problem, tree trace reconstruction, generalizes string trace reconstruction, which corresponds to the tree…

Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…

Tree-child networks, one of the prominent network classes in phylogenetics, have been introduced for the purpose of modeling reticulate evolution. Recently, the first author together with Gittenberger and Mansouri (2019) showed that the…

Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…

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…

Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…

In a complex network, different groups of nodes may have existed for different amounts of time. To detect the evolutionary history of a network is of great importance. We present a general method based on spectral analysis to address this…

The C-Orientation problem asks whether it is possible to orient an undirected graph to a directed phylogenetic network of a desired network class C. This problem arises, for example, when visualising evolutionary data, as popular methods…

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…