Related papers: On Computing the Dollo-1 phylogeny in polynomial t…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…
Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…
This paper characterizes and discusses devolutionary genetic algorithms and evaluates their performances in solving the minimum labeling Steiner tree (MLST) problem. We define devolutionary algorithms as the process of reaching a feasible…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has…
One strategy for reconstruction of phylogenetic networks is to solve the phylogenetic network problem, which involves inferring phylogenetic trees first and subsequently computing the smallest phylogenetic network that displays all the…
An important problem in evolutionary biology is to reconstruct the evolutionary history of a set $X$ of species. This history is often represented as a phylogenetic network, that is, a connected graph with leaves labelled by elements in $X$…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
The maximum parsimony phylogenetic tree reconstruction problem is NP-hard, presenting a computational bottleneck for classical computing and motivating the exploration of emerging paradigms like quantum computing. To this end, we design…
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…
The inference of the evolutionary history of a collection of organisms is a problem of fundamental importance in evolutionary biology. The abundance of DNA sequence data arising from genome sequencing projects has led to significant…
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…
A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
In this paper we consider the problem of computing an mRNA sequence of maximal similarity for a given mRNA of secondary structure constraints, introduced by Backofen et al. in [BNS02] denoted as the MRSO problem. The problem is known to be…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
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…
Phylogenetic Diversity(PD)is a well-regarded measure of the overall biodiversity of a set of present-day species(taxa)that indicates its ecological significance.In the Maximize Phylogenetic Diversity(Max-PD)problem one is asked to find a…