Related papers: Neighbor Joining Plus - algorithm for phylogenetic…
In evolutionary biology, phylogenetic trees are commonly inferred from a set of characters (partitions) of a collection of biological entities (e.g., species or individuals in a population). Such characters naturally arise from molecular…
Rooted phylogenetic networks are used by biologists to infer and represent complex evolutionary relationships between species that cannot be accurately explained by a phylogenetic tree. Tree-child networks are a particular class of rooted…
A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for reconstructing trees, it is crucial to understand the size and structure of the…
In evolutionary biology, networks are becoming increasingly used to represent evolutionary histories for species that have undergone non-treelike or reticulate evolution. Such networks are essentially directed acyclic graphs with a leaf set…
In recent decades, phylogenetic networks have become a standard tool in modeling evolutionary processes. Nevertheless, basic combinatorial questions about them are still largely open. For instance, even the asymptotic counting problem for…
It is a known fact that, given two rooted binary phylogenetic trees, the concept of maximum acyclic agreement forests is sufficient to compute hybridization networks with minimum hybridization number. In this work, we demonstrate by first…
Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…
A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all…
We propose a partitioning of the set of unlabelled, connected cubic graphs into two disjoint subsets named genes and descendants, where the cardinality of the descendants is much larger than that of the genes. The key distinction between…
Background: The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly…
We address phylogenetic reconstruction when the data is generated from a mixture distribution. Such topics have gained considerable attention in the biological community with the clear evidence of heterogeneity of mutation rates. In our…
Galled trees are studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into tree-child, galled and reticulation-visible network classes by relaxing a structural condition imposed on…
Two genes are xenologs in the sense of Fitch if they are separated by at least one horizontal gene transfer event. Horizonal gene transfer is asymmetric in the sense that the transferred copy is distinguished from the one that remains…
The ancestral maximum-likelihood and phylogeography problems are two fundamental problems involving evolutionary studies. The ancestral maximum-likelihood problem involves identifying a rooted tree alongside internal node sequences that…
Polyploidization is an evolutionary process by which a species acquires multiple copies of its complete set of chromosomes. The reticulate nature of the signal left behind by it means that phylogenetic networks offer themselves as a…
We consider the reconciliation problem, in which the task is to find a mapping of a gene tree into a species tree, so as to maximize the likelihood of such fitting, given the available data. We describe a model for the evolution of the…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…
The supertree construction problem is about combining several phylogenetic trees with possibly conflicting information into a single tree that has all the leaves of the source trees as its leaves and the relationships between the leaves are…
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…