Related papers: Inference of maximum parsimony phylogenetic trees …
Summary: GeneSupport implements a genome-scale algorithm: Maximum Gene-Support Tree to estimate species tree from gene trees based on multilocus sequences. It provides a new option for multiple genes to infer species tree. It is…
We study the problem of constructing phylogenetic trees for a given set of species. The problem is formulated as that of finding a minimum Steiner tree on $n$ points over the Boolean hypercube of dimension $d$. It is known that an optimal…
Computing an optimal classification tree that provably maximizes training performance within a given size limit, is NP-hard, and in practice, most state-of-the-art methods do not scale beyond computing optimal trees of depth three.…
One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first…
Tree search algorithms, such as branch-and-bound, are the most widely used tools for solving combinatorial and nonconvex problems. For example, they are the foremost method for solving (mixed) integer programs and constraint satisfaction…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
In conservation biology, phylogenetic diversity (PD) provides a way to quantify the impact of the current rapid extinction of species on the evolutionary `Tree of Life'. This approach recognises that extinction not only removes species but…
Reconciliation methods aim at recovering macro evolutionary events and at localizing them in the species history, by observing discrepancies between gene family trees and species trees. In this article we introduce an Integer Linear…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
A recent breakthrough by Ambainis, Balodis, Iraids, Kokainis, Pr\=usis and Vihrovs (SODA'19) showed how to construct faster quantum algorithms for the Traveling Salesman Problem and a few other NP-hard problems by combining in a novel way…
The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…
Phylogeny is the field of modelling the temporal discrete dynamics of speciation. Complex models can nowadays be studied using the Approximate Bayesian Computation approach which avoids likelihood calculations. The field's progression is…
The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large-scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their…
Evolutionary scenarios displaying reticulation events are often represented by rooted phylogenetic networks. Due to biological reasons, those events occur very rarely, and, thus, networks containing a minimum number of such events,…
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 define a new problem in comparative genomics, denoted PQ-Tree Search, that takes as input a PQ-tree $T$ representing the known gene orders of a gene cluster of interest, a gene-to-gene substitution scoring function $h$, integer…
Genetic algorithms are heuristic optimization techniques inspired by Darwinian evolution. Quantum computation is a new computational paradigm which exploits quantum resources to speed up information processing tasks. Therefore, it is…
In computational phylogenetics, the problem of constructing a supertree of a given set of rooted input trees can be formalized in different ways, to cope with contradictory information in the input. We consider the Minimum Flip Supertree…
Stochastic models are highly relevant tools in science, engineering, and society. Recent work suggests emerging quantum computing technologies can substantially decrease the memory requirements for simulating stochastic models. Here we show…