The simplest scriptΒΆ

Section author: Gavin Huttley

This is just about the simplest possible Cogent script for evolutionary modelling. We use a canned nucleotide substitution model (the HKY85 model) on just three primate species. As there is only unrooted tree possible, the sequence names are all that’s required to make the tree.

>>> from cogent.evolve.models import HKY85
>>> from cogent import LoadSeqs, LoadTree
>>> model = HKY85()
>>> aln = LoadSeqs("data/primate_cdx2_promoter.fasta")
>>> tree = LoadTree(tip_names=aln.Names)
>>> lf = model.makeLikelihoodFunction(tree)
>>> lf.setAlignment(aln)
>>> lf.optimise()
>>> print lf
Likelihood Function Table
======
 kappa
------
5.9589
------
===========================
   edge    parent    length
---------------------------
  human      root    0.0040
macaque      root    0.0384
  chimp      root    0.0061
---------------------------
===============
motif    mprobs
---------------
    T    0.2552
    C    0.2581
    A    0.2439
    G    0.2428
---------------