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The maximum clade credibility chronogram and the summary of the divergence time estimates and clade supports (PP) generated by the BEAST software are shown in Figure 2 and Table 2 Figure 2 Maximum clade credibility chronogram estimated by BEAST.
The tree was obtained in TreeAnnotator from the BEAST software using a threshold for clade credibility of 0.5.
The Bayesian calculation consisted of 100,000,000 generations Markov Chains Monte Carlo (MCMC) with sampling every 10,000th generation using the BEAST software package version 1.4 [34].
The Bayesian calculation consisted of 50,000,000 generations Markov Chains Monte Carlo (MCMC) with sampling every 5000th generation using the BEAST software package version 1.4 (http://evolve.zoo.ox.ac.uk/beast/).ac.uk/beast/
The concatenated matrix was analyzed using BEAST software [42], [43], which uses a Metropolis-Hastings MCMC algorithm to simultaneously estimate evolutionary parameters, phylogeny, and divergence dates under a relaxed clock model.
To this end, the evolutionary rate was estimated by employing the Bayesian Markov Chains Monte Carlo (MCMC) clock method [34] implemented in the BEAST software package (http://evolve.zoo.ox.ac.uk/beast/).ac.uk/beast/
A time-scaled maximum clade credibility tree was inferred using the BEAST software package.
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Seasoned observers of the industry are impressed by his grasp of the complicated beast that is software.
All of the analyses described here are implemented in the open access software package BEAST 1.5.4 (http://beast-mcmc.googlecode.com/).
Source code implementing the cartographic models has been made fully available as part of the software package BEAST (Drummond et al., 2012), and can be downloaded from its Google code repository (http://code.google.com/p/beast-mcmc/).
But directory software is a different beast.
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