Lineage profiling (Tp)

Tp Mode - Lineage profiling

python3 Zombi.py Tp ./Parameters/SpeciesTreeParameters.tsv ./Output_folder

This mode allows the user to fine control the number of lineages per unit of time. The user must give in a line different times followed by the goal population size for each time, as in:

TIME1-LINEAGEGOAL1;TIME2-LINEAGEGOAL2; TIMEn-LINEAGEGOALn

For instance:

LINEAGE_PROFILE 100-200;300-15000;500-50

By running this, the simulation runs for 500 units of time. In the first 100 units of time, the lineage number goal is 200. First, as we have only one lineage alive at the beginning (the root), there will be only speciation events at the rate given by the user until the lineage number is attained. If the lineage number is attained before the time is 100, then the species tree will reach an equilibrium, in which there is a turnover of species at the rate given by the parameter TURNOVER. Then, after time 100, the new lineage number goal is 15000. The same process is repeated. Only speciations will take place until the new goal is attained. After time 300, the lineage number goal is 50. In this case, only extinctions will take place until this final goal is attained. The simulation will end up when time == 500

Parameters

TURNOVER

Specific for Tp mode, it controls the rate at which new species appear and disappear at the equilibrium. Each time a turnover takes place, two random lineages are chosen. One goes extinct and the other speciates.

LINEAGE_PROFILE

Specific for Tp mode, refer to the section above to understand