Comparison of methods for estimating the nucleotide substitution matrix

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Oscamou, Maribeth ^a   McDonald, Daniel ^b   Bing, Von Bing ^c   Huttley, Gavin A ^d   Lladser, Manuel E ^a   Knight, Rob ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b UCB 450   (United States)

^c NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^d Biology and Environment   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

COMPARISON OF METHODS; COMPUTATION TIME; EUCLIDEAN DISTANCE; MATHEMATICAL BASIS; MAXIMUM LIKELIHOOD METHODS; MOLECULAR EVOLUTION; NUCLEOTIDE SUBSTITUTION; ORDERS OF MAGNITUDE;

MOLECULAR BIOLOGY;

NUCLEOTIDES;

DNA; NUCLEOTIDE;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPARATIVE STUDY; COMPUTER SIMULATION; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROBABILITY; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; STATISTICAL ANALYSIS; STATISTICAL MODEL;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; DNA; DNA MUTATIONAL ANALYSIS; EVOLUTION, MOLECULAR; LOGISTIC MODELS; MARKOV CHAINS; MODELS, GENETIC; NUCLEOTIDES; PHYLOGENY; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY;

EID: 60849097564     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-511     Document Type: Article

References (36)

1. Kimura M Evolutionary rate at the molecular level Nature 1968, 217:129-624. 626 10.1038/217624a0 5637732
2. Lio P Goldman N Models of molecular evolution and phylogeny Genome Res 1998, 8(12):1233-1244. 9872979
3. Blouin M Yowell C Courtney C Dame J Substitution bias, rapid saturation, and the use of mtDNA for nematode systematics Mol Biol Evol 1998, 15:1719-1727. 9866206
4. Sueoka N On the genetic basis of variation and heterogeneity of DNA base composition Proc Natl Acad Sci USA 1962, 48:582-592. 220819 13918161 10.1073/pnas.48.4.582
5. Hori H Osawa S Origin and evolution of organisms as deduced from 5S ribosomal RNA sequences Mol Biol Evol 1987, 4:445-472. 2452957
6. Knight RD Freeland SJ Landweber LF A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes Genome Biol 2001, 2:4. RESEARCH0010 31479 11305938 10.1186/gb-2001-2-4-research0010
7. Lobry JR Asymmetric substitution patterns in the two DNA strands of bacteria Mol Biol Evol 1996, 13(5):660-665. 8676740
8. Lobry JR Sueoka N Asymmetric directional mutation pressures in bacteria Genome Biol 2002, 3-10. RESEARCH0058 134625 12372146 10.1186/ gb-2002-3-10-research0058
9. Huttley GA Modeling the impact of DNA methylation on the evolution of BRCA1 in mammals Mol Biol Evol 2004, 21(9):1760-1768. 10.1093/molbev/ msh187 15190129
10. Faith JJ Pollock DD Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes Genetics 2003, 165(2):735-745. 1462789 14573484
11. Francino MP Ochman H Isochores result from mutation not selection Nature 1999, 400(6739):30-1. 10.1038/21804 10403245
12. Sueoka N Wide intra-genomic G+C heterogeneity in human and chicken is mainly due to strand-symmetric directional mutation pressures: dGTP-oxidation and symmetric cytosine-deamination hypotheses Gene 2002, 300(1-2):141-54. 10.1016/S0378-1119(02)01046-6 12468095
13. Lake JA Phylogenetic inference: How much evolutionary history is knowable? Mol Biol Evol 1997, 14(3):213-219. 9066789
14. Ota R Penny D Estimating changes in mutational mechanisms of evolution J Mol Evol 2003, 57(Suppl 1):233-240. 10.1007/s00239-003-0032-1
15. Felsenstein J Evolutionary trees from DNA sequences: A maximum likelihood approach J Mol Evol 1981, 17(6):368-76. 10.1007/BF01734359 7288891
16. Posada D Crandall KA MODELTEST: Testing the model of DNA substitution Bioinformatics 1998, 14(9):817-8. 10.1093/bioinformatics/14.9.817 9918953
17. Posada D Crandall KA Selecting models of nucleotide substitution: An application to human immunodeficiency virus 1 (HIV-1) Mol Biol Evol 2001, 18(6):897-906. 11371577
18. Galtier N Gouy M Inferring phylogenies from DNA sequences of unequal base compositions Proc Natl Acad Sci USA 1995, 92(24):11317-21. 40623 7479987 10.1073/pnas.92.24.11317
19. Yang Z Roberts D On the use of nucleic acid sequences to infer early branchings in the tree of life Mol Biol Evol 1995, 12:451-458. 7739387
20. Galtier N Gouy M Inferring pattern and process: Maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis Mol Biol Evol 1998, 15(7):871-879. 9656487
21. Galtier N Tourasse N Gouy M A nonhyperthermophilic common ancestor to extant life forms Science 1999, 283:220-221. 10.1126/ science.283.5399.220 9880254
22. Foster P Modeling compositional heterogeneity Syst Biol 2004, 53:485-495. 10.1080/10635150490445779 15503675
23. Jayaswal V Robinson J Jermiin L Estimation of phylogeny and invariant sites under the general Markov model of nucleotide sequence evolution Syst Biol 2007, 56:155-162. 10.1080/10635150701247921 17454972
24. Foster PG Hickey DA Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions J Mol Evol 1999, 48(3):284-90. 10.1007/PL00006471 10093217
25. Jermiin L Ho SY Ababneh F Robinson J Larkum AW The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated Syst Biol 2004, 53(4):638-643. 10.1080/10635150490468648 15371251
26. Dayhoff MO Schwartz RM Orcutt BC A model of evolutionary change in proteins Atlas of Protein Sequence and Structure Washington DC: National Biomedical Research Foundation Dayhoff MO 1978, 5:345-352.
27. Waddell P Steel M General time-reversible distances with unequal rates across sites: Mixing gamma and inverse Gaussian distributions with invariant sites Mol Phylogenet Evol 1997, 8:398-414. 10.1006/ mpev.1997.0452 9417897
28. Goldman N Thorne JL Jones DT Using Evolutionary Trees in Protein Secondary Structure Prediction and Other Comparative Sequence Analysis J Mol Biol 1996, 263(2):196-208. 10.1006/jmbi.1996.0569 8913301
29. Kosiol C Goldman N Different Versions of the Dayhoff Rate Matrix Mol Biol Evol 2005, 22(2):193-199. 10.1093/molbev/msi005 15483331
30. Gojobori T Li W Graur D Patterns of nucleotide substitution in pseudogenes and functional genes J Mol Evol 1982, 18:360-369. 10.1007/ BF01733904 7120431
31. Hamady M Betterton MD Knight R Using the nucleotide substitution rate matrix to detect horizontal gene transfer BMC Bioinformatics 2006, 7:476. 1657035 17067382 10.1186/1471-2105-7-476
32. Knight R Maxwell P Birmingham A Carnes J Caporaso J Easton B Eaton M Hamady M Lindsay H Liu Z Lozupone C McDonald D Robeson M Sammut R Smit S Wakefield M Widmann J Wikman S Wilson S Ying H Huttley G PyCogent: A toolkit for making sense from sequence Genome Biol 2007, 8:R171. 2375001 17708774 10.1186/gb-2007-8-8-r171
33. Jayaswal V Jermiin L Robinson J Estimation of Phylogeny Using a General Markov Model Evol Bioinf Online 2005, 1:62-80.
34. Barry D Hartigan J Statistical Analysis of Hominoid Molecular Evolution Stat Sci 1987, 2(2):191-210. 10.1214/ss/1177013353
35. Chang J Full reconstruction of Markov models in evolutionary trees: identifiability and consistency Math Biosci 1995, 137(51):73. 10.1016/ S0025-5564(96)00075-2
36. Felsenstein J Inferring phylogenies Sunderland, MA: Sinauer Associates 2004.