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Generating Species Trees

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AADavin edited this page Nov 21, 2018 · 22 revisions

Basic Mode (T)

Zombi uses a Birth-death model to generate a species tree. Lineages can speciate given rise to two new lineages or go extinct over time. The usage is:

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

Output

CompleteTree.nwk The complete species tree including the dead lineages, in newick format

ExtantTree.nwk The surviving species tree, in newick format

Events.tsv: Events (speciation and extinction) taking place in the species tree

Parameters

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. Otherwise is ignored

N_LINEAGES

To use in combination with the stopping rule 1. Otherwise is ignored

MIN_LINEAGES

When using with the stopping rule 0, if the alive lineages in the tree are <= MIN_LINEAGES the run will be considered a failure and the program will start again

MAX_LINEAGES

If the run attains this number of lineage the simulation is killed ant the program will start again

SPECIATION, EXTINCTION

Rates of evolution for the different events

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

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