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This is a user-friendly program for setting the evolutionary model and options for the MCMC analysis.

The second step is to actually run BEAST using the input file that contains the data, model and settings.

These issues can be addressed and hopefully overcome by employing comprehensive taxon sampling, large numbers of characters, multiple data sets (derived from different sources), and diverse inferential techniques.

In spite of being limited to samples of only living or recently extinct taxa, molecular data have great potential to help decipher the pattern and timing of rapid and ancient radiations.

These dating results appeared to be robust against some conditional changes for time estimation, such as gene regions used, taxon representation, and data partitioning.

The Bayesian estimation of divergence times without assuming the molecular clock suggested the Jurassic divergence of Eublepharidae from Gekkonidae and radiations of most eublepharid genera around the Cretaceous.

These models open the gate to a new field of "relaxed phylogenetics." Here we introduce a new approach to performing relaxed phylogenetic analysis.

Rapid evolutionary radiations characterize many higher-level taxa.

This pattern of diversification poses a challenge for accurate phylogenetic reconstruction, since the few synapomorphies defining short internal branches are often overwritten over long periods of evolutionary time, making determination of homology difficult and rendering the outgroup method of rooting prone to error for both molecular and morphological systematic investigations ().

We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data.

In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme.