Related papers: Fast error-tolerant quartet phylogeny algorithms
Reticulate evolutionary processes result in phylogenetic histories that cannot be modeled using a tree topology. Here, we apply methods from topological data analysis to molecular sequence data with reticulations. Using a simple example, we…
We present a simple $O(n^4)$-time algorithm for computing optimal search trees with two-way comparisons. The only previous solution to this problem, by Anderson et al., has the same running time, but is significantly more complicated and is…
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…
Topological phylogenetic trees can be assigned edge weights in several natural ways, highlighting different aspects of the tree. Here the rooted triple and quartet metrizations are introduced, and applied to formulate novel fast methods of…
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…
We present a deterministic algorithm that given a tree T with n vertices, a starting vertex v and a slackness parameter epsilon > 0, estimates within an additive error of epsilon the cover and return time, namely, the expected time it takes…
Network reconstruction consists in determining the unobserved pairwise couplings between $N$ nodes given only observational data on the resulting behavior that is conditioned on those couplings -- typically a time-series or independent…
We give a quasipolynomial-time algorithm for learning stochastic decision trees that is optimally resilient to adversarial noise. Given an $\eta$-corrupted set of uniform random samples labeled by a size-$s$ stochastic decision tree, our…
It is common in phylogenetics to have some, perhaps partial, information about the overall evolutionary tree of a group of organisms and wish to find an evolutionary tree of a specific gene for those organisms. There may not be enough…
In this paper we propose a dynamic data structure that supports efficient algorithms for updating and querying singly connected Bayesian networks (causal trees and polytrees). In the conventional algorithms, new evidence in absorbed in time…
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…
Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe…
In this paper, we have developed a fully-dynamic algorithm for maintaining cardinality of maximum-matching in a tree using the construction of top-trees. The time complexities are as follows: 1. Initialization Time: $O(n(log(n)))$ to build…
Evolutionary events such as incomplete lineage sorting and lateral gene transfer constitute major problems for inferring species trees from gene trees, as they can sometimes lead to gene trees which conflict with the underlying species…
One of the main aims of phylogenetics is to reconstruct the \enquote{Tree of Life}. In this respect, different methods and criteria are used to analyze DNA sequences of different species and to compare them in order to derive the…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
Trees are fundamental data structure for many areas of computer science and system engineering. In this report, we show how to ensure eventual consistency of optimistically replicated trees. In optimistic replication, the different replicas…
This paper presents two different efficiency-enhancement techniques for probabilistic model building genetic algorithms. The first technique proposes the use of a mutation operator which performs local search in the sub-solution…
Phylogenetic reconciliation seeks to explain host-symbiont co-evolution by mapping parasite trees onto host trees through events such as cospeciation, duplication, host switching, and loss. Finding an optimal reconciliation that ensures…
Reliability is one of the important measures of how well the system meets its design objective, and mathematically is the probability that a system will perform satisfactorily for at least a given period of time. When the system is…