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Example sentences for: mrbayes
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For the genome quartet #8 we calculated posterior probabilities under the model which takes ASRV into account with Strimmer and von Haeseler's [ 24 ] approach and with the MrBayes program version 2.01 [ 31 ] . TREE-PUZZLE 5.0 [ 56 ] was used to calculate posterior probabilities according to Strimmer and von Haeseler [ 24 ] . A discrete approximation of the gamma distribution [ 57 ] was used to describe ASRV.
Prior distributions for all parameters were the default distributions incorporated in the MrBayes software.
The same high support for this unexpected grouping is also recovered in bootstrap analysis and in posterior probabilities calculated with MrBayes [ 31 ] .
Comparing figure 4Bwith 4Ait is clear that in this case the Bayesian posterior probabilities estimated with MrBayes are more conservative assessments of reliability than the ones calculated according to [ 24 ] . The 99% support level calculated according to [ 24 ] approximately corresponds to the 90% support level calculated with MrBayes.
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).
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