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I analyzed the same data using the Bayesian program of Rannala and Yang (2003), using the gamma prior G 2, 2,000) for all θs and τHCG ∼ G 2, 300) with mean 0.0067.
Pairs of orthologous proteins were aligned using the ClustalW program [ 21] and their substitution (evolutionary) rates were calculated using the gamma distance correction [ 22].
The Hungarian scientists are using the gamma method to compare pottery from eight sites with a variety of clay samples in hope of establishing where the pots arose.
Rate heterogeneity among sites was modelled using the gamma model.
The priors were set using the gamma-Dirichlet prior [ 56].
The Bayesian tree was inferred using the MrBayes program, version 3.1.2 [44] with the GTR+ gamma correction model.
A preliminary maximum-likelihood tree was constructed using the FastTree program with default parameters (JTT evolutionary model, discrete gamma model with 20 rate categories [ 19]) [ 19].
A preliminary tree was constructed using the FastTree program with default parameters (JTT evolutionary model, discrete gamma model with 20 rate categories) [ 33].
Phylogenetic analysis was performed using the FastTree program with default parameters (JTT evolutionary model, discrete gamma model with 20 rate categories) [ 27].
The resulting 160-column alignment was used to construct a maximum likelihood phylogenetic tree using the FastTree program with default parameters (JTT evolutionary model, discrete gamma model with 20 rate categories) [ 31].
Likelihood searches were performed in a Bayesian framework under the JTT-f substitution model accommodating site rate variation (fraction of invariable sites plus four variable gamma rates) using the program MrBayes [ 55].
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