Sentence examples for nodes were inferred from inspiring English sources
After the architectures of these outer nodes were inferred, they were treated as leaves to initiate another round of ancestral architecture-inferring process until the ancestral architectures at all inner nodes were inferred, after which gene duplication/loss and fusion/loss events were inferred and dated.
The support values for the internal nodes were inferred by 1000 bootstrap replicates.
Results of divergence date estimates from individual genes showed that the oldest dates for all nodes were inferred from the wg gene and the youngest dates for all nodes were inferred from the 18S gene with r8s (Table 2).
Ancestral sequences for all interior nodes were inferred based on empirical Bayesian methods implemented in the CODEML program in the PAML 4.4 package [ 55].
The hidden states of the protein nodes were inferred using a Gibbs-sampling-based belief propagation in the EM algorithm, i.e. Monte Carlo EM algorithm (MCEM) [ 42].
The logical relationships linking in the new nodes were inferred from published data on the wiring of the S.cerevisiae cell cycle [ 25].
Branch support for internal nodes was inferred by bootstrapping 1000 replicates in PAUP*.
Thus, the extant species are labelled with the binding site predictions and the inner nodes are inferred by parsimony.
Gain or loss of these motifs at tree nodes was inferred by parsimony ancestral reconstruction using the combined N- and C-terminal domain trees in MacClade 4.0 [ 54].
Bayesian support for the nodes was inferred in MrBAYES using 4 × 106 Markov Chain Monte Carlo (MCMC) steps after convergence was reached, discarding a very conservative 50% of the samples as burn-in.
Relative support for tree nodes was inferred from Bayesian posterior probabilities estimated from all trees sampled once the average standard deviation of split frequencies had converged on a stable value, as well as through 100 nonparametric ML bootstrap replicates.
