First, we simulated SMPs with α = 0.1, 0.2, 1, and 10 under neutral scenario, we then analyzed the distribution of Dm, Dmod, and D computed with α = 0.5 based on the SMPs (supplementary table S5, Supplementary Material online).
Based on the ANI (supplementary table S1, Supplementary Material online) we were able to assign all analyzed strains into six groups, which correspond to five Vibrio species with validly published names and one previously undescribed species.
Comparative analysis of the set of putative Streptococcus virulence genes from Davies et al. (2007) (211 orthologous genes) resulted in a similar clustering to that based on the VFDB (supplementary fig. S7- B, Supplementary Material online).
Based on the new supplementary difference sets, we also provide E fNOD -optimal multi-lE fNOD -optimalated designs with a large number of columns when compared with other desupersaturated
On the other hand, two slightly different copies of each Python V1ra1 and V1r2 were successfully amplified from Pantherophis guttatus genomic DNA using primers based on the Python sequences (supplementary file S7, Supplementary Material online).
Function was predicted for each gene family based on the COG database (supplementary fig. S6, Supplementary Material online).
Based on the tree topology (supplementary fig. S4, Supplementary Material online), this second copy results from a gene duplication event before the radiation of the T. hominis/V.
Based on the data in the supplementary table S1 (Supplementary Material online) of Jiang and Machado (2009), we categorized genes as being male or female biased in D. pseudoobscura if their expression levels differed at least 2-fold in the two sexes, and q, the measure of statistical significance of this difference, was less than 10−.
The IFS curves plotted based on the data of Supplementary S3 are shown in Figure 1.
