Seqsim Simple Tree Simulation

Section author: Julia Goodrich

This is an example of how to use the birth-death model in cogent to simulate a tree.

>>> from cogent.seqsim.birth_death import BirthDeathModel, ExtinctionError,\
... TooManyTaxaError

Create a model with specific death probabilities per timestep using BirthProb and DeathProb, and TimePerStep. The desired maximum number of taxa on the tree can be set using MaxTaxa.

>>> b = BirthDeathModel(BirthProb=0.2, DeathProb=0.1, TimePerStep=0.03,
... MaxTaxa=20)

To simulate a tree with an exact number of taxa, use the following loop. The exact flag raises a TooManyTaxaError exception if the call produces the wrong number of taxa (e.g. because too many things died in the same timestep). An ExtinctionError is raised if the ancestral node dies off, or all the nodes die off.

>>> while True:
...     try:
...         t = b(exact=True)
...     except (ExtinctionError, TooManyTaxaError):
...         pass
...     else:
...         break

t now contains a RangeNode tree object that was returned, and can be used the same ways any other tree object in cogent is used. For instance, seqsim can be used to evolve alignments.