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Logo plots [ 54] showing cysteine codon bias were constructed using Geneious software, version 5.4.
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A small percentage of sequences from each non-focal clade are not expected to strongly bias the resulting assemblies because contigs were constructed using the consensus sequence at each base position.
In addition, and as a related issue, the study may have introduced a reporting or same source bias, as the area-specific measures were constructed using variables from the same study population as the health data.
The 95% confidence intervals for the Kappa coefficient were constructed using the bias-corrected percentile method [ 35, 36].
These estimates were constructed using output from CMAQ, bias-corrected with monitoring network data, as detailed in Hogrefe et al. (2009).
Phylogenetic trees were constructed using MEGA3 [73].
Kymographs were constructed using Metamorph 7.1.4 software.
Neighbor-joining trees were constructed using NEIGHBOR.
Strains were constructed using standard genetic techniques.
Maps were constructed using maps2WinBUGS version 1.6.
Figures and movies were constructed using CHIMERA [98].
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