-
Notifications
You must be signed in to change notification settings - Fork 5
Home
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 explained in each of the following sections:
The parameters are read from a .tsv file that it can be modified with any text editor.
Some of the parameters accept variable values. Those parameters can be easily seen in the parameters file because they have values composed of a letter and some numbers. For instance:
SPECIATION f:4 EXTINCTION n:2,0.5
The letter before the colon indicates the type of distribution (f fixed, u uniform, n normal, l lognormal)
If you launch SimuLyon in the mode T with the next parameters, the speciation rate will be 4, and the extinction rate will be sampled once at the beginning from a normal distribution of mean 2 and standard deviation 0.5. Watch out! If the sampled value is negative, the returned value will be the absolute value