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| Nylander JA, Wilgenbusch JC, Warren DL, et al. (2008) AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics (Oxford, England). 24: 581-3 |
| Beier BA, Nylander JA, Chase MW, et al. (2004) Phylogenetic relationships and biogeography of the desert plant genus Fagonia (Zygophyllaceae), inferred by parsimony and Bayesian model averaging. Molecular Phylogenetics and Evolution. 33: 91-108 |
| Irestedt M, Fjeldså J, Nylander JA, et al. (2004) Phylogenetic relationships of typical antbirds (Thamnophilidae) and test of incongruence based on Bayes factors. Bmc Evolutionary Biology. 4: 23 |
| Nylander JA, Ronquist F, Huelsenbeck JP, et al. (2004) Bayesian phylogenetic analysis of combined data. Systematic Biology. 53: 47-67 |