Reliabilities of parsimony-based and likelihood-based methods for detecting positive selection at single amino acid sites
| Autor: | Yoshiyuki Suzuki, Masatoshi Nei |
|---|---|
| Rok vydání: | 2001 |
| Předmět: |
Likelihood Functions
Phylogenetic tree Models Genetic Maximum likelihood Positive selection Contrast (statistics) Inference Biology Antigen recognition site Evolution Molecular Amino Acid Substitution HLA Antigens Statistics Genetics False positive paradox Humans Single amino acid Selection Genetic Molecular Biology Ecology Evolution Behavior and Systematics |
| Zdroj: | Molecular biology and evolution. 18(12) |
| ISSN: | 0737-4038 |
| Popis: | The reliabilities of parsimony-based and likelihood-based methods for inferring positive selection at single amino acid sites were studied using the nucleotide sequences of human leukocyte antigen (HLA) genes, in which positive selection is known to be operating at the antigen recognition site. The results indicate that the inference by parsimony-based methods is robust to the use of different evolutionary models and generally more reliable than that by likelihood-based methods. In contrast, the results obtained by likelihood-based methods depend on the models and on the initial parameter values used. It is sometimes difficult to obtain the maximum likelihood estimates of parameters for a given model, and the results obtained may be false negatives or false positives depending on the initial parameter values. It is therefore preferable to use parsimony-based methods as long as the number of sequences is relatively large and the branch lengths of the phylogenetic tree are relatively small. |
| Databáze: | OpenAIRE |
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