Evidence map›Paper›PMID 31705189›Full record

ArticleJournal of mathematical biology2020

Embeddability and rate identifiability of Kimura 2-parameter matrices.

Marta Casanellas, Jesús Fernández-Sánchez, Jordi Roca-Lacostena

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Article in Journal of mathematical biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

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3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Article
  2. Embedding of Markov matrices forJournal of mathematical biology · 2024
    Article
  3. Article
  4. Article
  5. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Marta CasanellasDpt. Matemàtiques, Universitat Politècnica de Catalunya and BGSMath, Diagonal 647, 08028, Barcelona, Spain. marta.casanellas@upc.edu.ORCID 0000-0002-1724-8358
Jesús Fernández-SánchezDpt. Matemàtiques, Universitat Politècnica de Catalunya and BGSMath, Diagonal 647, 08028, Barcelona, Spain.
Jordi Roca-LacostenaDpt. Matemàtiques, Universitat Politècnica de Catalunya and BGSMath, Diagonal 647, 08028, Barcelona, Spain.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Deciding whether a substitution matrix is embeddable (i.e. the corresponding Markov process has a continuous-time realization) is an open problem even for [Formula: see text] matrices. We study the embedding problem and rate identifiability for the K80 model of nucleotide substitution. For these [Formula: see text] matrices, we fully characterize the set of embeddable K80 Markov matrices and the set of embeddable matrices for which rates are identifiable. In particular, we describe an open subset of embeddable matrices with non-identifiable rates. This set contains matrices with positive eigenvalues and also diagonal largest in column matrices, which might lead to consequences in parameter estimation in phylogenetics. Finally, we compute the relative volumes of embeddable K80 matrices and of embeddable matrices with identifiable rates. This study concludes the embedding problem for the more general model K81 and its submodels, which had been initiated by the last two authors in a separate work.

Indexed as

Models, GeneticMutation RatePhylogenyEvolution, MolecularMarkov ChainsMathematical ConceptsMutationNucleotidesNucleotidesEmbedding problemMarkov generatorMarkov matrixMatrix logarithmNucleotide substitution modelRate identifiability

Identifiers

PMID31705189

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.