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Example sentences for: mrbayes
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Because bootstrap analysis using ML is not computationally feasible for large data sets [ 85 ] , we conducted a Bayesian analysis as an alternative employing optimization parameters similar to the nucleotide substitution model that we used for ML [ 86 87 ] . The distinction between ML and Bayesian inference is that Bayesian provides probabilities for hypotheses, not probabilities of data given a hypothesis [ 85 87 88 ] . Bayesian analysis uses Markov Chain Monte Carlo (MCMC) methods to approximate posterior probability distributions that are a direct estimation of branch support because they are the true probabilities of the resulting clades under the assumed models, unlike bootstrap values [ 87 88 ] . Additionally, bootstrap values and posterior probabilities derived from Bayesian analyses for multiple data sets appear to be correlated [ 88 ] . The Bayesian analysis was conducted with the software MrBayes 2.0 [ 89 ] . A GTR substitution model with 6 rate frequencies was selected as the most similar model to the Trn+G substitution model (the latter model is not available in MrBayes).
The same high support for this unexpected grouping is also recovered in bootstrap analysis and in posterior probabilities calculated with MrBayes [ 31 ] .
Prior distributions for all parameters were the default distributions incorporated in the MrBayes software.
For calculation of posterior probabilities with MrBayes at least 25,000 cycles were used.
Posterior probabilities were also calculated with MrBayes version 2.01 [ 31 ] . Each QuartOP was analyzed with two simultaneous Markov chains for 25,000 cycles under the JTT substitution model [ 55 ] without ASRV.
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