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Systematic Biology, ISSN 1063-5157, 11/2019
Abstract A central objective in biology is to link adaptive evolution in a gene to structural and/or functional phenotypic novelties. Yet most analytic methods... 
Journal Article
Methods in molecular biology (Clifton, N.J.), 2019, Volume 1910, p. 3
Organisms display astonishing levels of cell and molecular diversity, including genome size, shape, and architecture. In this chapter, we review how the genome... 
Journal Article
Bioinformatics, ISSN 1367-4803, 08/2019, Volume 35, Issue 15, pp. 2545 - 2554
Abstract Motivation Likelihood ratio tests are commonly used to test for positive selection acting on proteins. They are usually applied with thresholds for... 
LIKELIHOOD RATIO TEST | SUBSTITUTION | HOMOGENEITY | BIOCHEMICAL RESEARCH METHODS | POWER | AMINO-ACID SITES | ACCURACY | GENE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | MATHEMATICAL & COMPUTATIONAL BIOLOGY | PHYLOGENETIC MIXTURE MODEL | ADAPTIVE EVOLUTION | IDENTIFIABILITY
Journal Article
Methods in molecular biology (Clifton, N.J.), 2019, Volume 1910, p. 399
Codon substitution models (CSMs) are commonly used to infer the history of natural section for a set of protein-coding sequences, often with the explicit goal... 
Journal Article
Current protocols in bioinformatics, 06/2016, Volume 54, p. 6.15.1
This unit provides protocols for using the CODEML program from the PAML package to make inferences about episodic natural selection in protein-coding... 
Computational Biology - methods | Likelihood Functions | Codon - chemistry | Selection, Genetic | Software | Evolution, Molecular
Journal Article
Current Protocols in Molecular Biology, ISSN 1934-3639, 2013, Issue 101, p. 19.1
Journal Article
PloS one, 2011, Volume 6, Issue 9, p. e24127
The mechanism of oxidative phosphorylation is well understood, but evolution of the proteins involved is not. We combined phylogenetic, genomic, and structural... 
Amino Acid Sequence | Phosphorylation | Salmon | Genomics | Molecular Conformation | Molecular Sequence Data | Mitochondria - metabolism | Phylogeny | Sequence Analysis, DNA | Biological Evolution | Sequence Homology, Amino Acid | Animals | Bayes Theorem | Oxygen - chemistry | Proton Pumps - physiology | Adenosine Triphosphate - chemistry | Evolution, Molecular
Journal Article
Methods in Molecular Biology, ISSN 1064-3745, 2018, Volume 1849, pp. 267 - 289
Microbial samples taken from an environment often represent mixtures of communities, where each community is composed of overlapping assemblages of species.... 
Supervised learning | Cross-validation | Prediction error | Predictive model | MCMC | OTU abundance | Microbial community structure | Hierarchical Bayesian model | Microbiome
Journal Article
Current protocols in molecular biology, 01/2013, Volume Chapter 19, p. Unit 19.1.
The field of molecular evolution, which includes genome evolution, is devoted to finding variation within and between groups of organisms and explaining the... 
Proteins - genetics | Animals | Base Sequence | Computer Simulation | Humans | Selection, Genetic | Molecular Sequence Data | Models, Genetic | Software | Codon - genetics | Phylogeny | Evolution, Molecular
Journal Article
MOLECULAR BIOLOGY AND EVOLUTION, ISSN 0737-4038, 06/2018, Volume 35, Issue 6, pp. 1473 - 1488
Journal Article
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