Modeling mitochondrial protein evolution using structural information

Journal of Molecular Evolution

Volumn 54, Issue 4, 2002, Pages 519-529

  Liò, Pietro ^a   Goldman, Nick ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Hidden Markov models; Maximum likelihood; Mitochondria; Models of evolution; Phylogeny; Transmembrane proteins

Indexed keywords

MEMBRANE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; MAMMAL; MITOCHONDRION; MOLECULAR EVOLUTION; PHYLOGENY; PROTEIN SECONDARY STRUCTURE;

EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; MITOCHONDRIAL PROTEINS; MODELS, BIOLOGICAL; PHYLOGENY; PROTEIN STRUCTURE, SECONDARY;

EUTHERIA; FUNGI; MAMMALIA; PROTISTA;

EID: 0036213764     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-001-0052-7     Document Type: Article

References (50)

1. Model of amino acid substitution in proteins encoded by mitochondrial DNA
2. Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA
3. The genome sequence of Rickettsia prowazekii and the origin of mitochondria
4. Phylogenetic relationships among vertebrate orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene
5. Conflict among individual mitochondrial proteins in resolving the phylogeny of vertebrate orders
6. Best-fit maximum-likelihood models for phylogenetic inference: Empirical tests with known phylogenies
7. A model of evolutionary change in proteins
8. A model of evolutionary change in proteins
9. Statistical tests of models of DNA substitution
10. Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics
11. Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses
12. Assessing the impact of secondary structure and solvent accessibility on protein evolution
13. Performance of phylogenetic methods in simulation
14. Phylogeny estimation and hypothesis testing using maximum likelihood
15. Phylogenetic methods come of age: Testing hypotheses in an evolutionary context
16. The rapid generation of mutation data matrices from protein sequences
17. A mutation data matrix for transmembrane proteins
18. Models of natural mutations including site heterogeneity
19. Using physical-chemistry-based substitution models in phylogenetic analyses of HIV-1 subtypes
20. An ancestral mitochondrial DNA resembling a eubacterial genome in miniature
21. Models of molecular evolution and phylogeny
22. Using protein structural information in evolutionary inference: Transmembrane proteins
23. How molecules evolve in eubacteria
24. Mutation accumulation in transfer RNAs: Molecular evidence for Muller's ratchet in mitochondrial genomes
25. Mutation accumulation in nuclear, organelle and prokaryotic transfer RNA genes
26. Substitution rates of organelle and nuclear genes in sharks: Implicating metabolic rate (again)
27. Body size, metabolic rate, generation time, and the molecular clock
28. Structure and organization of the mitochondrial genome of the unicellular red alga Cyanidioschuzon merolae deduced from the complete nucleotide sequence
29. Inferring the historical patterns of biological evolution
30. Phylogeny of eukaryotes based on ribosomal RNA: Long-branch attraction and models of sequence evolution
31. A tutorial on hidden Markov models and selected applications in speech recognition
32. Transmembrane helices predicted at 95% accuracy
33. Topology prediction for helical transmembrane proteins at 86% accuracy
34. A hidden Markov model for predicting transmembrane helices in protein sequences
35. Phylogenetic inference
36. Correct and incorrect vertebrate phylogenies obtained by the entire mitochondrial DNA sequences
37. Combining protein evolution and secondary structure
38. Principles governing amino acid composition of integral membrane proteins: Application to topology prediction
39. Why mitochondria need a genome
40. A general empirical model of protein evolution derived from multiple protein families using a maximum likelihood approach
41. Molecular phylogenetics: State-of-the-art methods for looking into the past
42. Function and evolution of a minimal plastid genome from a non-photosynthetic parasitic plant
43. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
44. Maximum-likelihood models for combined analyses of multiple sequence data
45. Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation
46. Maximum likelihood trees from DNA sequences: A peculiar statistical estimation problem
47. Models of amino acid substitution and applications to mitochondrial protein evolution
48. Estimation of primate speciation dates using local molecular clocks
49. Performance of likelihood ratio tests of evolutionary hypotheses under inadequate substitution models