Specifying and using an unrestricted nucleotide substitution model

Section author: Gavin Huttley

Do standard cogent3 imports.

>>> from cogent3 import LoadSeqs, LoadTree, DNA
>>> from cogent3.evolve.predicate import MotifChange
>>> from cogent3.evolve.substitution_model import Nucleotide

To specify substitution models we use the MotifChange class from predicates. In the case of an unrestricted nucleotide model, we specify 11 such MotifChanges, the last possible change being ignored (with the result it is constrained to equal 1, thus calibrating the matrix). Also note that this is a non-reversible model and thus we can’t assume the nucleotide frequencies estimated from the alignments are reasonable estimates for the root frequencies. We therefore specify they are to be optimised using optimise_motif_probs argument.

>>> ACTG = list('ACTG')
>>> preds = [MotifChange(i, j, forward_only=True) for i in ACTG for j in ACTG if i != j]
>>> del(preds[-1])
>>> preds
[A>C, A>T, A>G, C>A, C>T, C>G, T>A, T>C, T>G, G>A, G>C]
>>> sm = Nucleotide(predicates=preds, recode_gaps=True,
...                 optimise_motif_probs=True)
>>> print(sm)

Nucleotide ( name = ''; type = 'None'; params = ['A>C', 'A>T', 'A>G',...

We’ll illustrate this with a sample alignment and tree in data/primate_cdx2_promoter.fasta.

>>> al = LoadSeqs("data/primate_cdx2_promoter.fasta", moltype=DNA)
>>> al
3 x 1525 dna alignment: human[AGCGCCCGCGG...], macaque[AGC...
>>> tr = LoadTree(tip_names=al.names)
>>> print(tr)
(human,macaque,chimp)root;

We now construct the parameter controller with each predicate constant across the tree, get the likelihood function calculator and optimise the function.

>>> lf = sm.make_likelihood_function(tr, digits=2, space=3)
>>> lf.set_alignment(al)
>>> lf.set_name('Unrestricted model')
>>> lf.optimise(local=True, show_progress=False)

We just used the Powell optimiser, as this works quite well.

>>> print(lf)
Unrestricted model
log-likelihood = -2491.7870
number of free parameters = 17
==========================================================================
 A>C    A>G    A>T    C>A    C>G    C>T    G>A    G>C    T>A    T>C    T>G
--------------------------------------------------------------------------
0.49   4.88   1.04   2.04   0.99   7.89   9.00   1.55   0.48   5.53   1.57
--------------------------------------------------------------------------
=========================
   edge   parent   length
-------------------------
  human     root     0.00
macaque     root     0.04
  chimp     root     0.01
-------------------------
==============
motif   mprobs
--------------
    T     0.26
    C     0.26
    A     0.24
    G     0.24
--------------

This data set consists of species that are relatively close for a modest length alignment. As a result, doing something like allowing the parameters to differ between edges is not particularly well supported. If you have lots of data it makes sense to allow parameters to differ between edges, which can be specified by modifying the lf as follows.

>>> for pred in preds:
...     lf.set_param_rule(pred, is_independent=True)

You would then re-optimise the model as above.