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Figure 2 | BMC Evolutionary Biology

Figure 2

From: Reducing the false positive rate in the non-parametric analysis of molecular coevolution

Figure 2

Testing the effect of different parameters in the percentage of positive values (PPV, plots a to c) and sensitivity (SN, plots d to f) of Mutual Information Criterion based methods to detect coevolution when parsimony filtering is applied. We tested the effect on PPV and SN of variations in the size of the multiple sequences alignment (MSAs, with the sizes ranging between 20 and 100 sequences), mean pairwise amino acid distance (with distances ranging between 0.1 and 2 amino acid substitutions per site) and strength of coevolution (the level of coevolution ranged between a minimum of 10% and a maximum of 25%). Coevolution levels indicate the distribution of patterns of coevolution at a particular pairs of amino acid sites. For example levels of 10% indicate that 10% of sequences at that particular pair of sites in the multiple sequence alignment correlate in one amino acid state pattern whereas the 90% remaining correlate in a different state. The strongest levels of coevolution (those showing highest MI values) will be presented by those pairs of sites showing 25% of coevolution strength.

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