Related papers: Defining binary phylogenetic trees using parsimony
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
We present an axiomatic framework for analyzing the algorithmic properties of decision trees. This framework supports the classification of decision tree problems through structural and ancestral constraints within a rigorous mathematical…
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 define a new balance index for rooted phylogenetic trees based on the symmetry of the evolutive history of every set of 4 leaves. This index makes sense for multifurcating trees and it can be computed in time linear in the number of…
The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…
Phylogenetic trees are important tools in the study of evolutionary relationships between species. Measures such as the index of Sackin, Colless, and Total Cophenetic have been extensively used to quantify tree balance, one key property of…
Phylogenetic trees are binary nonplanar trees with labelled leaves, and plane oriented recursive trees are planar trees with an increasing labelling. Both families are enumerated by double factorials. A bijection is constructed, using the…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
We propose a novel method for the inference of phylogenetic trees that utilises point configurations on hyperbolic space as its optimisation landscape. Each taxon corresponds to a point of the point configuration, while the evolutionary…
In biology, a phylogenetic tree is a tool to represent the evolutionary relationship between species. Unfortunately, the classical Schr\"oder tree model is not adapted to take into account the chronology between the branching nodes. In…
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…
Recently, considerable effort has been put into developing fast algorithms to reconstruct a rooted phylogenetic network that explains two rooted phylogenetic trees and has a minimum number of hybridization vertices. With the standard…
The parsimony score of a character on a tree equals the number of state changes required to fit that character onto the tree. We show that for unordered, reversible characters this score equals the number of tree rearrangements required to…
Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. The…
Measures of tree balance play an important role in different research areas such as mathematical phylogenetics or theoretical computer science. The balance of a tree is usually quantified in a single number, called a balance or imbalance…
Reticulate evolution gives rise to complex phylogenetic networks, making their interpretation challenging. A typical approach is to extract trees within such networks. Since Francis and Steel's seminal paper, "Which Phylogenetic Networks…
Phylogenetic networks are a flexible model of evolution that can represent reticulate evolution and handle complex data. Tree-based networks, which are phylogenetic networks that have a spanning tree with the same root and leaf-set as the…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
While every rooted binary phylogenetic tree is determined by its set of displayed rooted triples, such a result does not hold for an arbitrary rooted binary phylogenetic network. In particular, there exist two non-isomorphic rooted binary…