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Parameters
You can change the parameters directly in the tsv files. Watch out, it is a tabular separated values file, so you do not want mess spaces and tabs. In the case you do not understand what a parameter does, you do not want to touch it.
STOPPING_RULE
- 0: Time stops arriving at TOTAL_TIME
- 1: Tree evolves until a total of species = N_LINEAGES (alive) have been generated
TOTAL_TIME
To use with the stopping rule 0
N_LINEAGES
To use in combination with the stopping rule 1. Otherwise is ignored
SPECIATION, EXTINCTION
Rates of evolution
DUPLICATION, TRANSFER, LOSS, INVERSION, TRANSLOCATION, ORIGINATION
The value for each type of event.
DUPLICATION_EXTENSION, TRANSFER_EXTENSION, LOSS_EXTENSION, INVERSION_EXTENSION, TRANSLOCATION_EXTENSION
The value of the p parameter of a geometric distribution that determines the extension of the genome (measured in number of genes) affected for event
REPLACEMENT_TRANSFER
A number between 0 and 1 controling the probability of replacement transfers (they only happen if there is a homologous position in the recipient genome)
STEM_FAMILIES
Number of gene families present in the ancestral genome at the root
MIN_GENOME_SIZE
The minimal size for a given genome. Smaller genomes will not be affected by losses events