Additional file 7.

Evolutionary rates analysis for all 3203 orthologous genes in B. bacteriovorus HD100 and Tiberius predicted by RSD. Substitution rates were estimated by pairwise comparison in PAML. Red highlighting denotes pairs with dS > 1.5, which indicates saturation of synonymous sites. Table title headings are as follows: ortholog pair (from RSD) = this is a code assigned by our in-house scripts; sites = number of nucleotides (minus the stop codon); dN = average number of nonsynonymous changes per nonsynonymous site; dNse = standard error of dN (calculated by the curvature method); dS = average number of synonymous changes per synonymous site; dSse = standard error of dS (calculated by the curvature method); lnL = likelihood of the evolutionary model used in PAML analysis; t = sequence distance estimated by maximum likelihood; kappa = estimated transition/transversion rate ratio; omega = dN/dS.

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Hobley et al. BMC Genomics 2012 13:670   doi:10.1186/1471-2164-13-670