Transition Probability

This applet plots Jukes-Cantor transition probilities, illustrating the effects of time and substitution rate on the amount of change experienced by a DNA sequence. Drag the rectangular slider with your mouse to simulate data corresponding to different times. The curve can be thought of as either (1) the probability of seeing state A at any particular site, or (2) the fraction of sites in state A. You can choose to start with a sequence with every site in state A, or a starting sequence in which no site is in state A. The rows and columns of the sequence have no meaning; think of this as one sequence of 500 nucleotides (not 10 sequences each 50 nucleotides long).