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Fig. 3 | BMC Evolutionary Biology

Fig. 3

From: Assessing parallel gene histories in viral genomes

Fig. 3

a,b Tree length (number of substitution per site) of TuMV. a Plot of the nucleotide tree length displaying the contribution of the first, second and third codon position in dark grey, white and light grey respectively. b Plot of the amino acid tree length. c,d Biplot of the principal coordinates analysis (PCoA) using the four variables TreeComp1_nt, TreeComp2_nt, TreeComp1_aa, TreeComp2_aa (see Additional file 5: Table S3) for TuMV. The first principal component is represented in the x-axis, and the second principal component is represented in the y-axis. Percentage values in the axes indicate the percentage of variation explained by either component. e Percentage of sites under positive (dark grey), neutral (white) and purifing selection (light grey) for TuMV (left scale). The solid black line represents the Huber M-estimator of ω (± median absolute deviation) of all positions for each gene and for the concatenated (right scale)

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