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Seqsim Simple Tree Simulation
=============================
.. sectionauthor:: Julia Goodrich
This is an example of how to use the birth-death model in cogent to simulate
a tree.
.. doctest::
>>> 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``.
.. doctest::
>>> 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.
.. doctest::
>>> 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.
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