Alignment-free phylogenetic reconstruction: Sample complexity via a branching process analysis

DOI10.1214/12-AAP852zbMath1377.92060arXiv1109.5002OpenAlexW3103262072MaRDI QIDQ1948701

Constantinos Daskalakis, Sebastien Roch

Publication date: 24 April 2013

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

Full work available at URL: https://arxiv.org/abs/1109.5002

zbMATH Keywords

branching processesalignmentphylogenetic reconstruction

Mathematics Subject Classification ID

Applications of branching processes (60J85) Interacting random processes; statistical mechanics type models; percolation theory (60K35) Genetics and epigenetics (92D10)

Related Items (8)

Unnamed Item ⋮ Impossibility of consistent distance estimation from sequence lengths under the TKF91 model ⋮ A note on probabilistic models over strings: the linear algebra approach ⋮ Identifiability of phylogenetic parameters from \(k\)-mer data under the coalescent ⋮ Phase transition in the sample complexity of likelihood-based phylogeny inference ⋮ Parametric analysis of alignment and phylogenetic uncertainty ⋮ Statistically consistent and computationally efficient inference of ancestral DNA sequences in the TKF91 model under dense taxon sampling ⋮ An impossibility result for phylogeny reconstruction from \(k\)-mer counts

Uses Software

• MAFFT
• CLUSTAL
• MUSCLE
• Bali-phy

Cites Work

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• A few logs suffice to build (almost) all trees (I)
• Inverting Random Functions II: Explicit Bounds for Discrete Maximum Likelihood Estimation, with Applications
• A memetic algorithm to schedule planned maintenance for the national grid
• Learning nonsingular phylogenies and hidden Markov models

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