Related papers: Constructing a Consensus Phylogeny from a Leaf-Rem…
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 generalize phylogenetic trees by allowing reticulate evolutionary events such as horizontal gene transfer and hybridization. Among the many subclasses of phylogenetic networks, orchard networks have attracted…
We give a 2-approximation algorithm for the Maximum Agreement Forest problem on two rooted binary trees. This NP-hard problem has been studied extensively in the past two decades, since it can be used to compute the rooted Subtree…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
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…
Orthology and paralogy relations are often inferred by methods based on gene similarity, which usually yield a graph depicting the relationships between gene pairs. Such relation graphs are known to frequently contain errors, as they cannot…
We analyse a maximum-likelihood approach for combining phylogenetic trees into a larger `supertree'. This is based on a simple exponential model of phylogenetic error, which ensures that ML supertrees have a simple combinatorial description…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
The phylogenetic tree construction is to infer the evolutionary relationship between species from the experimental data. However, the experimental data are often imperfect and conflicting each others. Therefore, it is important to extract…
Consensus maximization is widely used for robust fitting in computer vision. However, solving it exactly, i.e., finding the globally optimal solution, is intractable. A* tree search, which has been shown to be fixed-parameter tractable, is…
Species trees represent the historical divergences of populations or species, while gene trees trace the ancestry of individual gene copies sampled within those populations. In cases involving rapid speciation, gene trees with topologies…
Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…
There are multiple factors which can cause the phylogenetic inference process to produce two or more conflicting hypotheses of the evolutionary history of a set X of biological entities. That is: phylogenetic trees with the same set of leaf…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
We present a new method for inferring species trees from multi-copy gene trees. Our method is based on a generalization of the Robinson-Foulds (RF) distance to multi-labeled trees (mul-trees), i.e., gene trees in which multiple leaves can…
The standard approach to estimate species trees is to align a selected set of genes, concatenate the alignments and then estimate a consensus tree. However, individual genes contain differing levels of evolutionary information, either…
In this paper, we consider the problem of reconstructing trees from traces in the tree edit distance model. Previous work by Davies et al. (2019) analyzed special cases of reconstructing labeled trees. In this work, we significantly expand…
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…
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…
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…