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Phylogenetic systematics and biogeography of hummingbirds: Bayesian and maximum likelihood analyses of partitioned data and selection of an appropriate partitioning strategy.
Fig. 9 Phylogeny of publicly available crustacean and selected invertebrate opsins based on maximum likelihood analyses of amino acid residues.
Maximum parsimony and maximum likelihood analyses were carried out.
Similar conclusions were reached using Maximum Likelihood analyses.
Maximum likelihood analyses based on the combined dataset provided strong support for an A. means+A.
Maximum likelihood analyses were performed in RAxML 7.0.4 [36], using 1000 replications.
The resulting trees of Bayesian and Maximum Likelihood analyses were rooted on midpoint.
Phylogenetic maximum likelihood analyses were performed with RAxML v.7.0.4 [28].
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Admixture graphs and residuals from maximum-likelihood analyses were used to model the contribution of migration and gene flow to genetic structure19.
Each of the constrained models were compared to the best fit model on the basis of log-likelihood values (maximum-likelihood analyses in BayesTraits), log-Bayes factors (MCMC analyses in BayesTraits) or LRT and Akaike information criterion scores (maximum-likelihood analyses of BiSSE model in diversitree 38,39,78,79.
Maximum-likelihood analyses were performed using PhyML [ 67].
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