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When α is estimated using the data, one approach is to use π (R = r | C, α ^ ) where R = (R R1,…, R R m )′, however, this method does not take into account the variability introduced by the model parameters estimate.
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Table 5 presents a summary of model parameters estimated from laboratory and back-calculation in this study.
Also, each topology generated by RAxML and GARLI has unique model parameters estimated with it.
The GTR+Γ model of nucleotide substitution was used with model parameters estimated on an initial neighbour-joining tree.
Then PAUP* was used to calculate the same likelihoods using the optimal model parameters estimated by GARLI.
Figure 10 shows the final posterior distributions on the four model parameters estimated from the data during one simulation of the epidemic under adaptive management.
Thus PAUP* was used to calculate likelihoods using the optimal model parameters estimated by RAxML for all of the tree topologies generated in RAxML and GARLI.
MtDNA data for individual mouse lemurs were concatenated and analyzed in a two-partition framework with model parameters estimated separately for the cox2 and cytb genes.
As described previously [ 43], we employed for this analysis model parameters estimated for the human proteome.
Model parameters estimated on three biological data sets and used for generating DNA sequences.
All free model parameters were estimated with RAxML, with GAMMA model parameters estimated up to an accuracy of 0.1 log likelihood units.
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