Ugene is an open source package that incorporates HMM ( hidden Markov models ) and so I am trying out this package and intend to delve into the source a bit. It fits in the general interest in Markov chains and how it is implemented, and how it is applied in unique ways.

I am really impressed with the code, the methods and the interface. Very **very** talented designers. Below is a chromatogram which represents the automatic sequencing output which looks a lot like a fluorescent Sanger using a primer, which I have done. High throughput and parallel methods have since been implemented and direct view using my in vivo atomic microscope can be faster. Thus some probabilistic interpretation is in order, and a lot of overlap or multiple runs.

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