Genome Representation

A file can contain several genomes. The first genome is used for the simulation process. A genome starts with a > followed by the genome name. In the following line(s) come the genes. 'Newlines' do not matter. Each chromosome is concluded by ) or |. A ) concludes a circular chromosome, a | concludes a linear chromosome. The gene names can contain all signs except whitespaces. A - before a gene name means that the gene direction is backwards. Every line that starts with // has no function and is a comment-line. Everything before the first genome is a comment, too. Example:

a c -d | b e ) f g |

A simple example file can be found here. A more complex example file that shows the possibilities can be found here.

Tree Representation

A tree file can only contain one tree. Comments can be made via starting a line with //. The tree must be represented in the NEWICK representation.

Program Usage - Step By Step

• First choose a genome file with the "Choose Genome-File" Button. Instead by select the checkbox "Genome random" CheckBox in the Random section it is possible to generated a random genome. For a genome which should be generated random two additionally parameters can be choosen.
  • The number of chromosomes the genome should have.
  • The average length each chromosome of the genome should have.
• Second choose a tree file with the "Choose Tree-File" Button or select a random generation by selecting the " Guidetree random" CheckBox.
• Third choose the rearrangement operations which should be used during the simulation process. Also the operations can be selected to be used random. Therefor select the " Operations random" CheckBox in the Random Section. If operations are selected to each of them a quantum can be given with which the operation should be represented in the simulation process. The programm handles choosen operations as follows:
  • If operations are chosen and no quantum is given to them, all operations have the same quantum: one.
  • Otherwise if operations are chosen and some of them have a given quantum while others have not, GEvolutionS only consider those with a given quantum.

The Output Format

GEvolutionS creates a multiple fasta formatted output of the generated genomes. They can be saved in a fasta formatted file. Additionally the program creates a visual colored output of the rearranged genomes which can be save as a .jpg file.