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.

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