ACG: Rapid inference of population history from recombining nucleotide sequences

BMC Bioinformatics

Volumn 14, Issue 1, 2013, Pages

  O'Fallon, Brendan D ^a  

^a ARUP LABORATORIES   (United States)

Author keywords

Ancestral recombination graph; ARG; Bayesian inference; Coalescent; Recombination

Indexed keywords

ANCESTRAL RECOMBINATION GRAPHS; ARG; BAYESIAN INFERENCE; COALESCENT; RECOMBINATION;

ALIGNMENT; BAYESIAN NETWORKS; DATA INTEGRATION; ESTIMATION; FORESTRY; INFERENCE ENGINES; NUCLEOTIDES; TREES (MATHEMATICS);

POPULATION STATISTICS;

ALIGNMENT; BIOLOGICAL POPULATIONS; DATA PROCESSING; ESTIMATION; FORESTRY; MATHEMATICS; NUCLEOTIDES; STATISTICS; TREES;

ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; COMPUTER PROGRAM; DNA SEQUENCE; GENETIC RECOMBINATION; METHODOLOGY; MOLECULAR EVOLUTION; MONTE CARLO METHOD; PEDIGREE; POPULATION DENSITY; PROBABILITY; SEQUENCE ALIGNMENT;

BAYES THEOREM; EVOLUTION, MOLECULAR; MARKOV CHAINS; MODELS, GENETIC; MONTE CARLO METHOD; PEDIGREE; POPULATION DENSITY; RECOMBINATION, GENETIC; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84873249733     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-40     Document Type: Article

References (16)

1. Yang Z, Rannala B. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol Biol Evol 1997, 14(7):717-724. 10.1093/oxfordjournals.molbev.a025811, 9214744.
2. Kuhner M. Coalescent genealogy samplers: windows into population history. Trends Ecol Evol 2008, 24(2):86-93.
3. Huelsenbeck JP, Ronquist F. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17(8):754-755. 10.1093/bioinformatics/17.8.754, 11524383.
4. Ronquist F, Huelsenbeck JP. MrBayes 3: phylogenetic inference under mixed models. Bioinformatics 2003, 19(12):1572-1574. 10.1093/bioinformatics/btg180, 12912839.
5. Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 2007, 7:214. 10.1186/1471-2148-7-214, 2247476, 17996036.
6. Hey J, Nielsen R. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc Natl Acad Sci USA 2007, 104:2785-2790. 10.1073/pnas.0611164104, 1815259, 17301231.
7. Kuhner M. LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics 2006, 22(6):768-770. 10.1093/bioinformatics/btk051, 16410317.
8. Griffiths RC, Marjoram P. Ancestral inference from samples of DNA sequences with recombination. J Comp Biol 1996, 3(4):479-502.
9. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981, 17:368-376. 10.1007/BF01734359, 7288891.
10. Green PJ. Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 1995, 82(4):711-732.
11. Metropolis N, Rosenbluth AW, Resonbluth MN, Teller AH, Teller E. Equations of state calculations by fast computing machines. J Chem Phys 1953, 21(6):1087-1092.
12. Rambaut A, Grassly N. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Bioinformatics 1997, 13(3):235-238.
13. Sabeti PC, Reich DE, Higgins JM, Levine HZP, Richter DJ, et al. Detecting recent positive selection in the human genome from haplotype structure. Nature 2002, 419:832-837. 10.1038/nature01140, 12397357.
14. Voight BF, Kudaravalli S, Wen X, Pritchard JK. A Map of recent positive selection in the human genome. PLoS Biol 2006, 4(3):e72. 10.1371/journal.pbio.0040072, 1382018, 16494531.
15. McVean G, Awadalla P, Fearnhead P. A coalescent-based method for detecting and estimation recombination from gene sequences. Genetics 2002, 160:1231-1241. 1462015, 11901136.
16. Felsenstein J. PHYLIP (phylogeny inference package) version 3.69. Distributed by the J. Felsenstein 1993, Seattle: Department of Genetics, University ofWashington.