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Figure 5 | BMC Bioinformatics

Figure 5

From: IDEA: Interactive Display for Evolutionary Analyses

Figure 5

Results display for analysis using more than two sequences. The output display for a 'site models' codeml analysis with three or more sequences includes a sortable data table (columns: dataset name, number of sequences, model(s) of evolution used, likelihood score, tree length, κ and ω), a graphical depiction of a gene's phylogenetic tree (right panel) and a display of selective pressure along a gene (bottom panel). Results for an analysis of 104 datasets of 15 species each under six different models of evolution (NSsites = 0, 1, 2, 3, 7 and 8) are (partially) shown. Check marks next to likelihood scores for the PIG-A gene (third dataset from top; ENSG00000165195) indicate positive results for likelihood ratio tests (LRTs) on nested models 1-2 and 7-8; details of LRTs are available on mouse over (teal and green box). The selective pressure display (lower panel) features, for each amino acid residue, a stacked bar chart of the probabilities that the degree of selective constraint on that residue falls into each of several ω classes indicated by the color legend. While most residues in the PIG-A protein are extremely conserved (they fall with high probability in the gray class, which has the lowest ω value), there is strong evidence that the residues on the 5' end of protein are evolving under positive selection (yellow class, which corresponds to ω > 1)

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