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There are three main modes to run simuLyon: T (species Tree), G (Genomes) and S (Sequences)

You must run the computations in sequential order. This means that: Computing genomes requires having computed previously a species tree computed with the mode T. Computing sequences requires having computed previously genomes with the mode G.

Each main mode has different advanced options. For example, it is possible to account for the variability in the rates of genome evolution with the modes Ga or Gb.

The parameters are read from a .tsv file that it can be modified with any text editor.

• Generating a Species Tree (T)

• Generating Genomes (G)

• Generating Sequences (S)