Related papers: Species tree inference from genomic sequences usin…
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 inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies…
Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species…
In this paper, we address the question of comparison between populations of trees. We study an statistical test based on the distance between empirical mean trees, as an analog of the two sample z statistic for comparing two means. Despite…
Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination…
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…
In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…
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 multispecies coalescent model describes the generation of gene trees from a rooted metric species tree, and thus provides a framework for the inference of species trees from sampled gene trees. We prove that the STAR method of Liu et…
Merge trees are a type of graph-based topological summary that tracks the evolution of connected components in the sublevel sets of scalar functions. They enjoy widespread applications in data analysis and scientific visualization. In this…
Geometric graphs appear in many real-world data sets, such as road networks, sensor networks, and molecules. We investigate the notion of distance between embedded graphs and present a metric to measure the distance between two geometric…
The class of self-nested trees presents remarkable compression properties because of the systematic repetition of subtrees in their structure. In this paper, we provide a better combinatorial characterization of this specific family of…
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…
In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has…
We provide time- and sample-efficient algorithms for learning and testing latent-tree Ising models, i.e. Ising models that may only be observed at their leaf nodes. On the learning side, we obtain efficient algorithms for learning a…
Motivation: While the majority of gene histories found in a clade of organisms are expected to be generated by a common process (e.g. the coalescent process), it is well-known that numerous other coexisting processes (e.g. horizontal gene…
Galled trees, directed acyclic graphs that model evolutionary histories with isolated hybridization events, have become very popular due to both their biological significance and the existence of polynomial time algorithms for their…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
One of the goals of phylogenetic research is to find the species tree describing the evolutionary history of a set of species. But the trees derived from geneti data with the help of tree inference methods are gene trees that need not…
Compatibility of phylogenetic trees is the most important concept underlying widely-used methods for assessing the agreement of different phylogenetic trees with overlapping taxa and combining them into common supertrees to reveal the tree…