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Numerical Optimization Techniques in Maximum Likelihood Tree Inference
- Source :
- Bioinformatics and Phylogenetics: Seminal Contributions of Bernard Moret, Tandy Warnow. Bioinformatics and Phylogenetics: Seminal Contributions of Bernard Moret, 29, Springer, pp.21-38, 2019, Computational Biology (COBO), 978-3-030-10837-3. ⟨10.1007/978-3-030-10837-3_2⟩, Bioinformatics and Phylogenetics ISBN: 9783030108366
- Publication Year :
- 2019
- Publisher :
- HAL CCSD, 2019.
-
Abstract
- International audience; In this chapter, we present recent computational and algorithmic advances for improving the inference of phylogenetic trees from the analysis of homologous genetic sequences under the maximum likelihood criterion. In particular, we detail how the use of matrix algebra at the core of Felsenstein’s pruning algorithm, combined with the architecture of modern day computer processors, leads to efficient techniques for optimizing edge lengths. We also discuss some properties of the likelihood function when considering the optimization of the parameters of mixture models that are used to describe the variation of rates-across sites .
- Subjects :
- 0106 biological sciences
Optimization
0303 health sciences
Phylogenetic tree
Computer science
Markov processes
[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]
Inference
Markov process
Variation (game tree)
Mixture model
[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy
010603 evolutionary biology
01 natural sciences
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
03 medical and health sciences
symbols.namesake
Core (graph theory)
symbols
Enhanced Data Rates for GSM Evolution
Likelihood function
Mixture models
Algorithm
030304 developmental biology
Maximum likelihood
Subjects
Details
- Language :
- English
- ISBN :
- 978-3-030-10837-3
978-3-030-10836-6 - ISBNs :
- 9783030108373 and 9783030108366
- Database :
- OpenAIRE
- Journal :
- Bioinformatics and Phylogenetics: Seminal Contributions of Bernard Moret, Tandy Warnow. Bioinformatics and Phylogenetics: Seminal Contributions of Bernard Moret, 29, Springer, pp.21-38, 2019, Computational Biology (COBO), 978-3-030-10837-3. ⟨10.1007/978-3-030-10837-3_2⟩, Bioinformatics and Phylogenetics ISBN: 9783030108366
- Accession number :
- edsair.doi.dedup.....ddcd4c9d8bed35b4c7518ca7ac92bc71