Related papers: Polynomial-Time Algorithms for Phylogenetic Infere…
Polyploidy is an important speciation mechanism, particularly in land plants. Allopolyploid species are formed after hybridization between otherwise intersterile parental species. Recent theoretical progress has led to successful…
We investigate a relaxation of the notion of treewidth-fragility, namely tree-independence-number-fragility. In particular, we obtain polynomial-time approximation schemes for independent packing problems on fractionally…
In the context of reconstructing phylogenetic networks from a collection of phylogenetic trees, several characterisations and subsequently algorithms have been established to reconstruct a phylogenetic network that collectively embeds all…
In this paper, we present new efficiently solvable cases of the Minimum Uncovering Branching problem, an optimization problem with applications in cancer genomics introduced by Hujdurovi\'c, Husi\'c, Milani\v{c}, Rizzi, and Tomescu in 2018.…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
We propose a reinforcement-learning algorithm to tackle the challenge of reconstructing phylogenetic trees. The search for the tree that best describes the data is algorithmically challenging, thus all current algorithms for phylogeny…
Good representations for phylogenetic trees and networks are important for optimizing storage efficiency and implementation of scalable methods for the inference and analysis of evolutionary trees for genes, genomes and species. We…
Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the…
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…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
Here we present a new fixed parameter tractable algorithm to compute the hybridization number r of two rooted, not necessarily binary phylogenetic trees on taxon set X in time (6^r.r!).poly(n)$, where n=|X|. The novelty of this approach is…
We observe $n$ sequences at each of $m$ sites, and assume that they have evolved from an ancestral sequence that forms the root of a binary tree of known topology and branch lengths, but the sequence states at internal nodes are unknown.…
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…
This paper discusses various types of constraints, difficulties and solutions to overcome the challenges regarding university course allocation problem. A hybrid evolutionary algorithm has been defined combining Local Repair Algorithm and…
Inferring probabilistic networks from data is a notoriously difficult task. Under various goodness-of-fit measures, finding an optimal network is NP-hard, even if restricted to polytrees of bounded in-degree. Polynomial-time algorithms are…
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…
In the PATH COVER problem, one asks to cover the vertices of a graph using the smallest possible number of (not necessarily disjoint) paths. While the variant where the paths need to be pairwise vertex-disjoint, which we call PATH…
A pangenome captures the genetic diversity across multiple individuals simultaneously, providing a more comprehensive reference for genome analysis than a single linear genome, which may introduce allele bias. A widely adopted pangenome…
There exist several methods dealing with the reconstruction of rooted phylogenetic networks explaining different evolutionary histories given by rooted binary phylogenetic trees. In practice, however, due to insufficient information of the…
The Dollo model for reconstructing evolutionary trees from binary characters has been proposed as a generalization of the infinite sites model, also known as the Perfect Phylogeny. In particular, the Dollo model is considered more realistic…