Words similar to trn
Example sentences for: trn
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Simulation studies have shown that ML is typically more accurate and robust than MP [ 81 82 ] . Thus an ML analysis of the data was conducted by employing an heuristic search in PAUP* using TBR branch swapping on a starting tree based on neighbor joining, ACCTRAN, and STEEPEST DESCENT under the TrN+G DNA substitution model [ 83 ] . This model was selected using a Hierarchical Likelihood Ratio Test (HLRT) in Modeltest version 3.06 [ 84 ] .
Likelihood parameters for the dataset were determined by Modeltest 3.06 for the TrN+G model, and included the following: base frequencies of A = 0.2482, C = 0.207, G = 0.2466, T = 0.2982; r-matrix values of A-C = 1.0000, A-G = 3.1857, A-T = 1.0000, C-G = 1.0000, C-T = 5.1655, G-T = 1.0000; and a gamma distribution of 0.5663.
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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