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************************************
Controlling third party applications
************************************
Existing supported apps
=======================
Alignment apps
--------------
clustalw and muscle
^^^^^^^^^^^^^^^^^^^
.. doctest::
>>> from cogent import LoadSeqs, DNA
>>> from cogent.app.clustalw import align_unaligned_seqs as clustal_aln
>>> from cogent.app.muscle import align_unaligned_seqs as muscle_aln
>>> seqs = LoadSeqs(filename='data/test2.fasta', aligned=False)
>>> aln1 = clustal_aln(seqs, DNA)
>>> aln2 = muscle_aln(seqs, DNA)
>>> aln1 == aln2
True
>>> from cogent.app.fasttree import build_tree_from_alignment
>>> tr = build_tree_from_alignment(aln1,moltype=DNA)
>>> print tr.asciiArt()
/-Mouse
|
---------|--NineBande
|
| /-DogFaced
\0.508---|
| /-HowlerMon
\0.752---|
\-Human
And if you have matplotlib installed you can draw the tree (see :ref:`draw-trees`).
.. note:: Tree output based on v2.0.1
.. TODO add in cross-ref to drawing usage example
BLAST
-----
See :ref:`blast-usage`.
|
