Additional file 1:

CA of human and avian influenza viruses with avian viral subtypes indicated by color. Each viral gene is displayed in a 3 dimensional representation. The X, Y and Z axes are arbitrary scales generated by the CA.

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Additional file 2:

Outliers are enclosed by open-boxes. Sequence numbers of outliers are indicated (see Additional file 3). Avian virus outliers are marked in red, while human virus outliers are in black.

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Additional file 3:

Descriptions of human and avian viral sequences that were marked as outliers in Additional file 2.

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Additional file 4:

Estimation of 3D coordinates of a viral sequence.

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Additional file 5:

Cross validation of CA of PB2 sequences. Sequences (N = 3366) were randomly assigned to 5 equal groups and CA was performed on any 4 of these dataset (i.e. 80% of the total sequences). Based on the weight generated from the train set, coordinates of the remaining 20% test dataset were predicted by applying the formula similar to the one as described in Additional file 4. Left column: Original graphs as described in Fig. 1A (Human PB2) and Additional file 1 (Avian PB2). Right column: Representative results generated from one of the test dataset.

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Additional file 6:

Comparison of the location of recent seasonal human influenza viruses in CA. Left: CA from figure 1 with the coordinates of the recent human H1 and H3 influenza sequences (year 2007 to 2009) predicted from the eigen vectors of the original CA. Right: A CA of the combined set of sequences from Figure 1 and the recent seasonal influenza sequences. Recent seasonal influenza sequences are marked in darker color.

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Additional file 7:

The ten sequences that were closest to each of the A/Brevig Mission/1/1918 genes.

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Additional file 8:

CA of seasonal human (H1-H3), human H5, swine, avian, canine (H3N8) and equine (H3N8) influenza viruses. Each viral gene is displayed in a 3 dimensional representation. The X, Y and Z axes are arbitrary scales generated by the CA.

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Additional file 9:

Overall codon usage of Influenza virus types and their hosts. Under-represented codons (RSCU < 0.6) are highlighted in grey, while the most commonly used codons are in bold.

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Additional file 10:

Codons with positive (R ≥ 0.5) and negative (R ≤ -0.5) correlations in codon usage over time of viral isolation in human H1N1, human H3N2 and avian influenza viruses.

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Additional file 11:

Correlation coefficient (R) between viral GC content and year of virus isolation.

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Additional file 12:

Correlation coefficient (R) between nucleotide usage at the third position of a codon and year of virus isolation.

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Additional file 13:

Changes in the correlation between codon usage in PB2 and that in human tissue-specific genes over time of viral isolation. The linear regression line and the correlation coefficient of each dataset are shown.

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