Invertibility of the TKF model of sequence evolution

DOI10.1016/J.MBS.2005.12.025MaRDI QIDQ2488650zbMATH OpenOpenAlexWikidataFDO

Authors Bhalchandra D. Thatte

Publication date 11 May 2006

Published in Mathematical Biosciences (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/q-bio/0608017

zbMATH Keywords

identifiabilityphylogeneticsMarkov chainsalignmentequationsordinary differentialDNA sequence evolution modelsgeneral homology structures

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Problems related to evolution (92D15) Computational methods for problems pertaining to biology (92-08)

Abstract: We consider character sequences evolving on a phylogenetic tree under the TKF91 model. We show that as the sequence lengths tend to infinity the the topology of the phylogenetic tree and the edge lengths are determined by any one of (a) the alignment of sequences (b) the collection of sequence lengths. We also show that the probability of any homology structure on a collection of sequences related by a TKF91 process on a tree is independent of the root location. Keywords: phylogenetics, DNA sequence evolution models, identifiability, alignment

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Cites work

• scientific article; zbMATH DE number 3243264 (Why is no real title available?)
• scientific article; zbMATH DE number 2247647 (Why is no real title available?)
• A few logs suffice to build (almost) all trees (I)
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• Reconstructing phylogenies from nucleotide pattern probabilities: A survey and some new results
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Cited in

(7)

• Convergence rate estimation for the TKF91 model of biological sequence length evolution
• Impossibility of consistent distance estimation from sequence lengths under the TKF91 model
• Pairwise sequence alignment at arbitrarily large evolutionary distance
• Large-Scale Multiple Sequence Alignment and Phylogeny Estimation
• Do tree split probabilities determine the branch lengths?
• Alignment-free phylogenetic reconstruction: Sample complexity via a branching process analysis
• Statistically consistent and computationally efficient inference of ancestral DNA sequences in the TKF91 model under dense taxon sampling

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Uses Software

• fastDNAml

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