Mathematica notebook containing analysis output from H1N1pdm09 viruses originating from human hosts.

The notebook contains, for each gene analysed: A histogram of amino acid lengths of analysed sequences;A plot of Shannon information versus the score (raw codon variability values) at each codon in the gene;An example sequence from the gene with nucleotide loci found to be constrained highlighted (in orange if found to be constrained without needing to adjust for potentially interfering regions, in blue if only found after adjusting for potentially interfering regions);A codon-level report of nucleotide usage (with observed and expected values for usage, mean distance, normalised ratio, weighted normalised ratio, weighted normalised ratio after all ratios across the gene are scaled to a mean of zero and variance of one, and ranking of the codon after weighting and scaling, with the scaled values highlighted in orange or blue if in constrained regions, similarly to the example sequence highlighting);A plot showing the proportion of sequences at each codon where the observed amino acid produced is the most common one;Plots showing the weighted constraint scores for each codon for the raw (unranked) and ranked analyses, plus plots of cumulative sums of these scores (again with codons in constrained regions highlighted orange or blue, similarly to the example sequence highlighting, and with codons with zero weight plotted with open triangles and with paler colours). A histogram of amino acid lengths of analysed sequences; A plot of Shannon information versus the score (raw codon variability values) at each codon in the gene; An example sequence from the gene with nucleotide loci found to be constrained highlighted (in orange if found to be constrained without needing to adjust for potentially interfering regions, in blue if only found after adjusting for potentially interfering regions); A codon-level report of nucleotide usage (with observed and expected values for usage, mean distance, normalised ratio, weighted normalised ratio, weighted normalised ratio after all ratios across the gene are scaled to a mean of zero and variance of one, and ranking of the codon after weighting and scaling, with the scaled values highlighted in orange or blue if in constrained regions, similarly to the example sequence highlighting); A plot showing the proportion of sequences at each codon where the observed amino acid produced is the most common one; Plots showing the weighted constraint scores for each codon for the raw (unranked) and ranked analyses, plus plots of cumulative sums of these scores (again with codons in constrained regions highlighted orange or blue, similarly to the example sequence highlighting, and with codons with zero weight plotted with open triangles and with paler colours). The zip file contains a copy of the notebook in Mathematica format and in pdf. (ZIP)