Related papers: Unifying Parsimonious Tree Reconciliation
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
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…
A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
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…
Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…
In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to event-labeled gene trees. Knowledge of the event labels…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
We study the problem of sharing as many branching conditions of a given forest classifier or regressor as possible while keeping classification performance. As a constraint for preventing from accuracy degradation, we first consider the one…
The architecture of eukaryotic coding genes allows the production of several different protein isoforms by genes. Current gene phylogeny reconstruction methods make use of a single protein product per gene, ignoring information on…
The nature inspired algorithms are becoming popular due to their simplicity and wider applicability. In the recent past several such algorithms have been developed. They are mainly bio-inspired, swarm based, physics based and…
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…
Here we introduce researchers in algebraic biology to the exciting new field of cophylogenetics. Cophylogenetics is the study of concomitantly evolving organisms (or genes), such as host and parasite species. Thus the natural objects of…
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.…
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…
Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…
Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in…
Co-evolution is a powerful problem-solving approach. However, fitness evaluation in co-evolutionary algorithms can be computationally expensive, as the quality of an individual in one population is defined by its interactions with many (or…
Survival analysis concerns the task of predicting the time until an event occurs. Often used in the medical field, survival analysis deals with incomplete (i.e., censored) data, for instance, from patients who did not experience the event…
Plant breeding programs use data obtained from multi-environment selection experiments to produce improved varieties with the ultimate aim of maintaining high levels of genetic gain. Selection accuracy can be improved with the use of…