All the other colors represent fitness levels inbetween the two extremes. Black pixels represent population elements with very low relative fitness where as pink pixels represent population elements with reletively high fitness levels. Each pixel can be one of several colors: black, red, orange, yellow, green, blue, purple, and pink. The pixel's color depicts the population element's relative fitness. Each pixel in the fitness map represents the relative fitness of a population element. The fitness map is the most important of all three MPGAfold Visualizer maps. In order for the linear conformation to form, the branched conformation must unfold (attain a worse fitness) and then fold into the linear conformation. Notice the energy barrier that forms between the two conformations. The blue pixels represent the branched conformation of HIV and the purple pixels represent the linear conformation of HIV. This particular Fitness map taken from a run of an HIV sequence.
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As population elements attain better fitness (by minimizing free energy) the color will shift towards pink. The Fitness map depicts the relative fitness of every single population element in an MPGAfold run as a pixel. The shifts in color directly correlate to what is occuring within the MPGAfold run and thus, represent the search for the optimal solution. In some instances, the viewer may see the population converge to one color or he or she may see two distinct colors appear and then compete with one another for dominance. As time progresses and the run advances in generation, it is possible to see large changes taking place across the array of pixels. For example, if a population element undergoes a change in topology and thus attains a better fitness, the pixel representing that sturcture will change color. The histogram depicts the distribution of pixels over the window's color gradient (which represents the window's specific range of data).Īs the MPGAfold run advances and the population undergoes changes, each pixel's color will be updated accordingly. The precise facts differ depending on the window and will be discussed later on. The color or shade of a pixel depicts certain facts about the population element it represents. The array represents the current population of the MPGAfold run and each pixel in that array represents a member of the population. Each window houses a vast array of pixels along with a histogram.
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These windows can be considered gateways that peer upon the information contained in an MPGAfold run. The main user interface of MPGAfold Visualizer consists of three different windows. MPGAfold Visualizer User Interface General Information