Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A

Journal of Molecular Evolution

Volumn 51, Issue 5, 2000, Pages 423-432

  Yang, Ziheng ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Large phylogenies; Maximum likelihood; Molecular adaptation; Nonsynonymous substitution; Phylogenetics; Positive selection; Synonymous substitution

Indexed keywords

VIRUS HEMAGGLUTININ;

ADAPTATION; ALGORITHM; ARTICLE; CODON; GENE SEQUENCE; GENETIC SELECTION; INFLUENZA VIRUS A; MOLECULAR EVOLUTION; PHYLOGENY; STATISTICAL MODEL; VIRUS GENE;

DARWINIA; HUMAN INFLUENZA VIRUS; INFLUENZA A VIRUS; INFLUENZA VIRUS; INFLUENZAVIRUS A; RNA VIRUSES;

EID: 0033692959     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002390010105     Document Type: Article

References (28)

1. MOLPHY version 2.3: Programs for molecular phylogenetics based on maximum likelihood
2. Rapid evolution in plant chitinases: Molecular targets of selection in plant-pathogen coevolution
3. Positive selection on the H3 hemagglutinin gene of human influenza virus A
4. Parallel evolution of drug resistance in HIV: Failure of nonsynonymous/synonymous substitution rate ratio to detect selection
5. Evolutionary trees from DNA sequences: A maximum likelihood approach
6. Long term trends in the evolution of H(3) HA1 human influenza type A
7. A codon-based model of nucleotide substitution for protein-coding DNA sequences
8. New methods for estimating the numbers of synonymous and nonsynonymous substitutions
9. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts
10. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
11. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
12. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
13. The neighbor-joining method: A new method for reconstructing phylogenetic trees
14. A method for detecting positive selection at single amino acid sites
15. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
16. Among-site rate variation and its impact on phylogenetic analyses
17. Maximum-likelihood models for combined analyses of multiple sequence data
18. PAML: A program package for phylogenetic analysis by maximum likelihood
19. Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites
20. Synonymous and nonsynonymous rate variation in nuclear genes of mammals
21. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
22. Codon-substitution models for heterogeneous selection pressure at amino acid sites
23. Genealogical evidence for positive selection in the nef gene of HIV-1