A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times

Bioinformatics

Volumn 18, Issue 1, 2002, Pages 115-123

  Seo, Tae Kun ^a,b   Thorne, Jeffrey L ^c   Hasegawa, Masami ^a,b   Kishino, Hirohisa ^d  

^a GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^b INSTITUTE OF STATISTICAL MATHEMATICS   (Japan)

^c NORTH CAROLINA STATE UNIVERSITY   (United States)

^d UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DATA ANALYSIS; EVOLUTIONARY RATE; GENE SEQUENCE; HUMAN IMMUNODEFICIENCY VIRUS 1; MATHEMATICAL ANALYSIS; METHODOLOGY; MOLECULAR CLOCK; MOLECULAR EVOLUTION; PRIORITY JOURNAL; SAMPLING; TIME; VIRUS GENE;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; RNA VIRUSES;

EID: 0036166770     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.1.115     Document Type: Article

References (41)

1. Predicting the evolution of human influenza A
2. Testing goodness of fit for the Poisson assumption when observations are not identically distributed
3. Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA
4. Estimating divergence times in the presence of an overdispersed molecular clock
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 century of tobamovirus evolution in an Australian population of Nicotiana glauca
8. Phylogenetic information and experimental design in molecular systematics
9. A codon-based model of nucleotide substitution for protein-coding DNA sequences
10. Maximum-likelihood approach for gene family evolution under functional divergence
11. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
12. Toward a more accurate time scale for the human mitochondrial DNA tree
13. Evolution of protein molecules
14. The antiretro-virus drug 3′-azido-3′-deoxythymidine increases the retrovirus mutation rate
15. RNA secondary structure prediction using stochastic context-free grammars and evolutionary history
16. Timing the ancestor of the HIV-1 pandemic strains
17. The molecular clock of HIV-1 unveiled through analysis of a known transmission history
18. Retrovirus mutation rates and their role in genetic variation
19. Testing for equality of evolutionary rates
20. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
21. Very slightly deleterious mutations and the molecular clock
22. Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters
23. Optimal sequencing strategies for surveying molecular genetic diversity
24. Estimating the rate of molecular evolution: Incorporating non-contemporaneous sequences into maximum likelihood phylogenies
25. Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under non-standard conditions
26. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection
27. The origin and evolution of Ebola and Marburg viruses
28. Simple methods for testing the molecular evolutionary clock hypothesis
29. On the overdispersed molecular clock
30. Statistical models of the overdispersed molecular clock
31. Phylogenetic test of the molecular clock and linearized trees
32. Initial genetic characterization of the 1918 'Spanish' influenza virus
33. Manganese cations increase the mutation rate of human immunodeficiency virus type 1 ex vivo
34. Assessing the Cretaceous superordinal divergence times within birds and placental mammals by using whole mitochondrial protein sequences and an extended statistical framework
35. Distributions of statistics used for the comparison of models of sequence evolution in phylogenetics
36. Evidence for higher rates of nucleotide substitution in rodents than in man
37. The Mantel-Haenszel statistics for the extended odds ratio in the negative binomial distribution
38. Codon-substitution models for heterogeneous selection pressure at amino acid sites