相关论文: Phase Transition in Distance-Based Phylogeny Recon…
We introduce a new distance-based phylogeny reconstruction technique which provably achieves, at sufficiently short branch lengths, a polylogarithmic sequence-length requirement -- improving significantly over previous polynomial bounds for…
Recent work has highlighted deep connections between sequence-length requirements for high-probability phylogeny reconstruction and the related problem of the estimation of ancestral sequences. In [Daskalakis et al.'09], building on the…
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…
Reconstructing evolutionary trees from molecular sequence data is a fundamental problem in computational biology. Stochastic models of sequence evolution are closely related to spin systems that have been extensively studied in statistical…
We consider the branch-length estimation problem on a bifurcating tree: a character evolves along the edges of a binary tree according to a two-state symmetric Markov process, and we seek to recover the edge transition probabilities from…
In many interesting cases the reconstruction of a correct phylogeny is blurred by high mutation rates and/or horizontal transfer events. As a consequence a divergence arises between the true evolutionary distances and the differences…
We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct…
The analysis of Belief Propagation and other algorithms for the {\em reconstruction problem} plays a key role in the analysis of community detection in inference on graphs, phylogenetic reconstruction in bioinformatics, and the cavity…
We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…
We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is…
As whole genomes become widely available, maximum likelihood and Bayesian phylogenetic methods are demonstrating their limits in meeting the escalating computational demands. Conversely, distance-based phylogenetic methods are efficient,…
For supercritical multitype branching processes in continuous time, we investigate the evolution of types along those lineages that survive up to some time t. We establish almost-sure convergence theorems for both time and population…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
Distance based algorithms are a common technique in the construction of phylogenetic trees from taxonomic sequence data. The first step in the implementation of these algorithms is the calculation of a pairwise distance matrix to give a…
Distance-based phylogenetic algorithms attempt to solve the NP-hard least squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree metric. The set of all dissimilarity maps is a Euclidean…
Latent tree graphical models are widely used in computational biology, signal and image processing, and network tomography. Here we design a new efficient, estimation procedure for latent tree models, including Gaussian and discrete,…
The Kesten-Stigum Theorem is a fundamental criterion for the rate of growth of a supercritical branching process, showing that an L log L condition is decisive. In critical and subcritical cases, results of Kolmogorov and later authors give…
Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly.…
The log-det distance between two aligned DNA sequences was introduced as a tool for statistically consistent inference of a gene tree under simple non-mixture models of sequence evolution. Here we prove that the log-det distance, coupled…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…