Related papers: On Computing the Dollo-1 phylogeny in polynomial t…
The Persistent Perfect phylogeny, also known as Dollo-1, has been introduced as a generalization of the well-known perfect phylogenetic model for binary characters to deal with the potential loss of characters. The problem of deciding the…
Recently, the perfect phylogeny model with persistent characters has attracted great attention in the literature. It is based on the assumption that complex traits or characters can only be gained once and lost once in the course of…
The binary perfect phylogeny model is too restrictive to model biological events such as back mutations. In this paper we consider a natural generalization of the model that allows a special type of back mutation. We investigate the problem…
The perfect phylogeny is one of the most used models in different areas of computational biology. In this paper we consider the problem of the Persistent Perfect Phylogeny (referred as P-PP) recently introduced to extend the perfect…
Evolutionary models used for describing molecular sequence variation suppose that at a non-recombining genomic segment, sequences share ancestry that can be represented as a genealogy--a rooted, binary, timed tree, with tips corresponding…
The so-called binary perfect phylogeny with persistent characters has recently been thoroughly studied in computational biology as it is less restrictive than the well known binary perfect phylogeny. Here, we focus on the notion of (binary)…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
The reconstruction of phylogenetic trees from mixed populations has become important in the study of cancer evolution, as sequencing is often performed on bulk tumor tissue containing mixed populations of cells. Recent work has shown how to…
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 $X$…
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…
In conservation biology, phylogenetic diversity (PD) provides a way to quantify the impact of the current rapid extinction of species on the evolutionary `Tree of Life'. This approach recognises that extinction not only removes species but…
The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…
Several algorithms build on the perfect phylogeny model to infer evolutionary trees. This problem is particularly hard when evolutionary trees are inferred from the fraction of genomes that have mutations in different positions, across…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
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…
We study a character-based phylogeny reconstruction problem when an incomplete set of data is given. More specifically, we consider the situation under the directed perfect phylogeny assumption with binary characters in which for some…
Cancers follow a clonal Darwinian evolution, with fitter subclones replacing more quiescent cells, ultimately giving rise to macroscopic disease. High-throughput genomics provides the opportunity to investigate these processes and determine…
Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…
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 phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…