HMMEd: Hidden Markov Model editor
HMMEd (the Hidden Markov Model editor) is a graphical application which allows to create and edit Hidden Markov Models. Supported are
- discrete emissions on arbitrary alphabets; this includes DNA, RNA, and amino acids, and
- continous scalar emissions.
Discrete emission probabilities, as well as transition probabilities can be graphically edited using pie charts with handles. Parameters can also be entered directly. HMM topology can be edited manually by adding/deleting states and connecting them with the mouse. Hierarchical models, i.e. super nodes corresponding to complete promoters or codon models in gene finding HMMs, will be supported. Currently, a visually pleasant layout has to be done by hand.
For models with continous emission, a graphical editor for mixtures of pdfs is under development. A screenshot from a working prototype is shown above. The handles underneath the pdfs change mean as well as other pdf parameters, the pie chart controls the mixture coefficients.
HMMEd is licensed under the GPL. Its based on code from Gato the graph animation toolbox.