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Cited by 57Genomics and Phylogenetic StudiesRNA and protein synthesis mechanismsGenetic diversity and population structure

Likelihood Calculation in Molecular Phylogenetics

Bryant, David, Galtier, Nicolas, Poursat, Marie-Anne·2005·Mathematics of Evolution and Phylogeny
DOI 10.1093/oso/9780198566106.003.0002
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Abstract

Likelihood estimation is central to many areas of the natural and physical sciences and has had a major impact on molecular phylogenetics. In this chapter we provide a concise review of some of the theoretical and computational aspects of likelihood-based phylogenetic inference. We outline the basic probabilistic model and likelihood computation algorithm, as well as extensions to more realistic models and strategics of likelihood optimization. We survey several of the theoretical underpinnings of the likelihood framework, reviewing research on consistency, identifiability, and the effect of model mis-specification, as well as advantages, and limitations, of likelihood ratio tests.

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Crossref · 10.1093/oso/9780198566106.003.0002

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  • Finding the best tree is an exceptionally difficult task because evaluation of each tree requires a considerable amount of calculations and because the number of candidate strictly bifurcating trees grows very rapidly with the number of sequences.

    “However, finding the best tree is an exceptionally difficult task because evaluation of each tree requires a considerable amount of calculations (Bryant et al. 2005) as well as because the number of candidate strictly bifurcating trees grows very rapidly with the number of sequences (Felsenstein 1978)—for example, there are ∼8 × 1021 possible rooted topologies for a set of 20 taxa.”

    From Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets (2018) · cites this paper as Bryant et al. 2005

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Authors
Bryant, D., Galtier, N., & Poursat, M.-A.
ORCID
Venue
Mathematics of Evolution and Phylogeny
Publisher
Oxford University PressOxford
Published
2005-02-24
Pages
33-62
DOI
10.1093/oso/9780198566106.003.0002
OpenAlex
W3032526099
Cited by
57
References
55
Citations by year
2023: 2 · 2022: 1 · 2021: 2 · 2020: 5 · 2019: 1 · 2017: 6 · 2016: 5 · 2014: 5 · 2013: 1 · 2012: 7
FWCI
6.95
Type
book chapter
Language
en
Open access
closed
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Keywords
likelihood estimation, molecular phylogeny, phylogenetic inference, likelihood maximization, consistency, identifiability, model misspecification, likelihood ratio test

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