An impossibility result for phylogeny reconstruction from k-mer counts

DOI10.1214/22-AAP1805MaRDI QIDQ2108911FDOQ2108911

Authors: Wai-Tong Louis Fan, Brandon Legried, Sebastien Roch 

Publication date: 20 December 2022

Published in: The Annals of Applied Probability (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/2010.14460

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zbMATH Keywords

phylogenetics\(k\)-merstatistical consistencyinformation-theoretic boundsMarkov models on trees

Mathematics Subject Classification ID

Statistical aspects of information-theoretic topics (62B10) Markov processes: estimation; hidden Markov models (62M05)

Cites Work

• Biological Sequence Analysis
• Phylogeny. Discrete and random processes in evolution
• Phase transition in the sample complexity of likelihood-based phylogeny inference
• Algorithms on Strings, Trees and Sequences
• Phase transition of the largest eigenvalue for nonnull complex sample covariance matrices
• Distributional regimes for the number of k -word matches between two random sequences
• An elementary proof of the local central limit theorem
• Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes.
• Broadcasting on trees and the Ising model.
• Full reconstruction of Markov models on evolutionary trees: identifiability and consistency.
• Taxonomy with confidence
• Title not available (Why is that?)
• Line-of-descent and genealogical processes, and their applications in population genetics models
• Recovering a tree from the leaf colourations it generates under a Markov model
• A few logs suffice to build (almost) all trees (I)
• Compound Poisson approximation: A user's guide
• Alignment-free phylogenetic reconstruction: Sample complexity via a branching process analysis
• Phase transitions in phylogeny
• Computational phylogenetics. An introduction to designing methods for phylogeny estimation
• Probability
• Consistency of a phylogenetic tree maximum likelihood estimator
• Necessary and sufficient conditions for consistent root reconstruction in Markov models on trees
• Identifiability of phylogenetic parameters from \(k\)-mer data under the coalescent
• Impossibility of consistent distance estimation from sequence lengths under the TKF91 model
• Optimal sequence length requirements for phylogenetic tree reconstruction with indels

Cited In (2)

• Impossibility of phylogeny reconstruction from $k$-mer counts
• Statistically consistent and computationally efficient inference of ancestral DNA sequences in the TKF91 model under dense taxon sampling

Uses Software

• Mash
• Eigenstrat

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