Figure 2

The GUI of HMMEditor. The top menu (File and View) allows user to open, save, and view HMM models. It also allows user to save visualized figures and sequence files. The tabs under the menu provide function to view HMM in different modes (traditional, null model, HMM Logo, and pure text). The main window under the tabs shows the visualized HMM connectivity. The numbers on the edges denote the transition probabilities. The pie chart at the bottom left shows the emission probabilities of a selected state (e.g. M2). The window at the bottom right visualizes a group of sequences. User can select each one or all them to align against the HMM.