**VisualizationApp** allows to plot conditional sequence logos with customized layout from previously learned iPMMs.

As "Input model" any successfully learned iPMM can be used and it does not matter which of the learned tools has produced it.

If "IUPAC" is enabled all nodes representing more than one symbol will be labeled by the corresponding IUPAC code.

If "Marginals" is disabled, the nucleotide stacks corresponding to the marginal distribution, which correspond to the traditional sequence logo, are hidden.

If "Trivial" is enabled, PCTs with only 1 leaf and corresponding nucleotide stacks are shown. While they do not contain any additional information compared to the traditional sequence logo, plotting them might be useful if "Marginals" is disabled.  

If "Pseudonodes" is enabled, all pseudonodes (PCT nodes that are labeled by the full alphabet and have a trivial subtree) are plotted so that all PCT leaves are located at the maximal depth.

If "IC scaled" is disabled, the nucleotide stacks are not scaled according to their information content, which can be helpful to perceive small differences in distributions that are rather close to uniform. 

If "Y labels" is enabled, short descriptions of the different plot elements are shown on the Y axis.

If "Grid" is disabled, the grid separating the individual plot elements is not plotted.

If "Positions" is disabled, the sequence position labels at the top of the plot is not plotted.

If "Context labels" is disabled, the individual context numbers are not plotted.

