AWTY (are we there yet?): A system for graphical exploration of MCMC convergence in Bayesian phylogenetics

Bioinformatics

Volumn 24, Issue 4, 2008, Pages 581-583

  Nylander, Johan A A ^a   Wilgenbusch, James C ^a   Warren, Dan L ^b   Swofford, David L ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; COMPUTER PROGRAM; INFORMATION SERVICE; MONTE CARLO METHOD; PHYLOGENETIC TREE; PHYLOGENY; POST HOC ANALYSIS; PRIORITY JOURNAL; PROBABILITY; RELIABILITY;

EID: 39149141072     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm388     Document Type: Article

References (15)

1. Brooks,S.P. and Gelman,A. (1998) General methods for monitoring convergence of iterative simulations. J. Comput. Graphi. Stat., 7, 434-455.
2. Drummond,A.J. and Rambaut,A. (2006) BEAST v1.4. http://beast.bio.ed.pc.uk/
3. Geweke,J. (1992) Evaluating the accuracy of sampling-based approaches to calculating posterior moments. In: Bernado,J.M. et al. (eds.) Bayesian Statistics 4. Clarendon Press, Oxford UK.
4. Hardaker,W. (2006) Getopt:GUI:Lon Version 0.62, and QWizard Version 3.03. http://www.cpan.org
5. Huelsenbeck,J.P. et al. (2002) Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol., 51, 673-688.
6. Nylander,J.A.A. et al. (2004) Bayesian phylogenetic analysis of combined data. Syst. Biol., 53, 47-67.
7. Penny,D. and Hendy,M.D. (1985) The use of tree comparison metrics. Systematic Zool., 34, 75-82.
8. Plummer,M. et al. (2006) CODA: Output analysis and diagnostics for Markov Chain Monte Carlo simulations. http://cran.Rproject.org
9. R Development Core Team (2006) R: A language and environment for statistical computing, R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org
10. Rambaut,A. and DrummondA.J. (2004) Tracer v1.3 http://evolve.zoo.ox.ac.uk/software.html
11. Ronquist,F. and Huelsenbeck,J.P. (2003) MRBAYES 3: Bayesian phylogenetic-inference under mixed models. Bioinformatics, 19 1572-1574.
12. Simon,D. and Larget,B. (2000) Bayesian analysis in molecular biology and evolution (BAMBE), version 2.03 beta Department of Mathematics and Computer Science, Duquesne University.
13. Swofford,D.L. (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts, USA.
14. Temple-Lang,D. (2006) RSPerl Version 0.83. http://www.omephat.org/RSperl
15. Williams,T. and Kelley,C. (2006) GNUPLOT, an interactive plotting program, Version 4.0. http://www.gnuplot.info