Divergence of DNA sequences

Your browser does not support Java, or Java is not enabled. Sorry!

Instructions

• Select a substitution model (default: type = JC)
• Select the number of data points to plot (default: n = 10)
• Select a sequence length (default: length = 1000)
• Select percent difference (%) or calculated distance (d) display (default: %)

How to interpret the graph

When the percent difference display is chosen, the vertical axis shows the percent difference between two sequences. The horizontal axis shows the expected number of substitutions per site (lambda*t). The blue dots show data simulated according to the chosen model of sequence evolution. The red line shows the results expected assuming a Jukes-Cantor (JC) model of substitution.

When the calculated difference display is chosen, the vertical axis shows the distance that would be calculated from the observed percent difference assuming a Jukes-Cantor (JC) model of substitution. The horizontal axis shows the expected number of substitutions per site (lambda*t). The blue dots show data simulated according to the chosen model of sequence evolution. The red dots show data that falls outside the plot boundaries. The red line is where points would be expected to fall if observed distances exactly matched the expected number of substitutions.

The parameter kappa of the Kimura 2-parameter model (K2P) determines the transition/transversion bias.

• kappa = 1 implies no transition/transversion bias, i.e., Jukes-Cantor type substitution.
• kappa = 2 transitions are twice as likely as transversions.
• kappa = 4 transitions are four times as likely as transversions.
• kappa = 8 transitions are eight times as likely as transversions.