The idea is to use Transducers, which act like pairHMM for simulating evolutionary events. Those Transducers should be based on grammars, so there also a need for a specific grammar and its parser.

• Introduction to Transducers - Mutation and Alignment
• Evolutionary HMMs represented by different Transducers
• Basic Information and Ideas for Usage of Transducers

• http://www.biowiki.org

• One //Superannotation // for all possible annotations
• User can create new Anootations using the Superannotation
• All evolutionary steps will be built from a set of parametririzable basic operations:
  • Insertion
  • Deletion
  • Duplication
  • Double-Cut-Join
  • Move (Transposon)
  • Substitution

  Transducer is sequence based 
  * Need of neutral state (no event) 
  * Step by step (base by Base) 

  Hierarchical annonations, tree like -- (Chromosome (Gen (Intron, Exon)), Transposon) 

• Mutationprobabilities (edges in phylotree (inverse probabilities) must be >= 1) will affect only outgoing edges from Match state
• Probabilities will be stored in matrices for each annotation and mutation
• Startingposition for Transposon/Satelites will be set automatically

• Automaton Modell definieren √
• Automaton Schnittstellen definieren & implementieren√
• Automaton fuer Character-Basierte Evolution erstellen √/X
• Automaton Controller erstellen √/X
• Join Automata √
• Import von konkreten Automata erstellen X
• Schnittstelle zum User Interface herstellen X
• Konkrete Automata fuer verschiedene Annotationen erstellen X

knapp 50% √

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