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. 2015 Jul 1;7(8):2117–2135. doi: 10.1093/gbe/evv129

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© The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Fig. 5.— — MDS plot of codon usage differences among HPVs. The different HPVs are classified by an unsupervised two-step clustering algorithm, and visualized by MDS dimension reduction. The clusters are colored yellow (cluster1), blue (cluster 2), and green (cluster 3), respectively. Cluster analysis has been conducted for each gene separately; for this reason, “cluster 1” represents a totally independent set of PVs for each gene. Each symbol represents one individual HPV, and the distance between points is proportional to the overall dissimilarity of CUPrefs. Codes for phenotypic presentation of the infection: Squares, mucocutaneous asymptomatic; dots, mucosal lesions; inverse triangles, genital warts; triangles, cutaneous warts.