Overview about the program

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