====== Overview about the program ======


===== How the program works =====

  * Given a phylogenetic tree and a root sequence, the program creates several automatons with specific parameters 
  * The automatons are transducers, which are markov chains that produces a sequence by the series of states 
  * In each state a operationfunction is called 
  * There are two different kindes of operationfunctions and transducers. One for sequence based operations and one for rearrangements. Both transducers are used to create a child sequence in the phylogenetic tree. 


===== How we work =====

  * If we add new functionality, we create JUnit-Tests to document what the code does 
  * Before commiting a new version, we have to make clear that the version is compilable 
  * For this purpose we have an ant skript, that we should execute before commiting