Related papers: Multi-SpaM: a Maximum-Likelihood approach to Phylo…
We consider the problem of constructing an an optimal-weight tree from the 3*(n choose 4) weighted quartet topologies on n objects, where optimality means that the summed weight of the embedded quartet topologiesis optimal (so it can be the…
The last decade brought a significant increase in the amount of data and a variety of new inference methods for reconstructing the detailed evolutionary history of various cancers. This brings the need of designing efficient procedures for…
Application of the turbo principle to multiuser decoding results in an exchange of probability distributions between two sets of constraints. Firstly, constraints imposed by the multiple-access channel, and secondly, individual constraints…
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…
Phylogenomics, even more so than traditional phylogenetics, needs to represent the uncertainty in evolutionary trees due to systematic error. Here we illustrate the analysis of genome-scale alignments of yeast, using robust measures of the…
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 Subtree…
Gene trees record the combination of gene level events, such as duplication, transfer and loss, and species level events, such as speciation and extinction. Gene tree-species tree reconciliation methods model these processes by drawing gene…
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…
Prediction suffix trees (PST) provide an effective tool for sequence modelling and prediction. Current prediction techniques for PSTs rely on exact matching between the suffix of the current sequence and the previously observed sequence. We…
We develop and analyze methods for computing provably optimal {\em maximum a posteriori} (MAP) configurations for a subclass of Markov random fields defined on graphs with cycles. By decomposing the original distribution into a convex…
We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our…
Distance-based approaches in phylogenetics such as Neighbor-Joining are a fast and popular approach for building trees. These methods take pairs of sequences from them construct a value that, in expectation, is additive under a stochastic…
Recovering a tree that represents the evolutionary history of a group of species is a key task in phylogenetics. Performing this task using sequence data from multiple genetic markers poses two key challenges. The first is the discordance…
The goal of the trace reconstruction problem is to recover a string $x\in\{0,1\}^n$ given many independent {\em traces} of $x$, where a trace is a subsequence obtained from deleting bits of $x$ independently with some given probability…
The Maximum Agreement Forest problem has been extensively studied in phylogenetics. Most previous work is on two binary phylogenetic trees. In this paper, we study a generalized version of the problem: the Maximum Agreement Forest problem…
Recent theoretical work has demonstrated that Neighbor Joining applied to concatenated DNA sequences is a statistically consistent method of species tree reconstruction. This brief note compares the accuracy of this approach to other…
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…
We consider the reconstruction of a phylogeny from multiple genes under the multispecies coalescent. We establish a connection with the sparse signal detection problem, where one seeks to distinguish between a distribution and a mixture of…
The problem of comparing trees representing the evolutionary histories of cancerous tumors has turned out to be crucial, since there is a variety of different methods which typically infer multiple possible trees. A departure from the…
In the trace reconstruction problem, the goal is to reconstruct an unknown string $x$ of length $n$ from multiple traces obtained by passing $x$ through the deletion channel. In the relaxed problem of $approximate$ trace reconstruction, the…