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In the latter systems context-dependent acoustic likelihoods were provided based on the answers to the phonetic context decoding questions.
For survival, the species-level likelihoods were binomial, and the hyperdistribution was a log-normal distribution of m.
The weights of the DAE and BF-DNN likelihoods were 0.6 and 0.4, respectively, corresponding to the settings in the development experiment.
Individual likelihoods were computed based on multinomial function that depends on r, p1 and p2.
Final assignment likelihoods were determined at the end of pass 3 calculations.
Marginal likelihoods were estimated as harmonic means of the sampled likelihoods in Tracer v. 1.5 [31], [31].
The likelihoods were calculated via a pruning algorithm, and an MCMC algorithm was implemented to traverse the parameter surfaces and locate the maxima.
For each tested tree, site likelihoods were calculated using CODEML and the AU test was performed using CONSEL [50] with default scaling and replicate values.
Likelihoods were computed with PAUP.
Site likelihoods were estimated with PAUP* [ 45].
Likelihoods were maximized numerically in Java.
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