Controlling third party applications

Existing supported apps

Alignment apps

clustalw and muscle

>>> 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 Drawing dendrograms and saving to PDF).

Note

Tree output based on v2.0.1

BLAST

See Controlling BLAST.

Phylo apps

To be written.

RNA structure apps

To be written.

Visualisation

To be written.

PyMol, MAGE

Adding new apps

To be written.

Pipelining 3rd party apps

To be written.