Additional file 2.

PAML Analysis of all Feather β-keratin Loci that Resulted in Positively Selected Sites: The six models are listed in the first column with a brief description, and the values obtained from each analysis are listed in their respective rows. The dN/dS ratios are the average of the sum of all branches. All positively selected sites above 95% are listed, with those reaching 99% shown in bold. The Naïve Empirical Bayes (NEB) and Bayes Empirical Bayes (BEB) are shown when appropriate. The M3 model only uses the NEB analysis [61]. Additionally, the tables for the likelihood ratio test (LRT) results for each locus are included (see Methods).

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Greenwold and Sawyer BMC Evolutionary Biology 2010 10:148   doi:10.1186/1471-2148-10-148