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.
Adding new apps¶
To be written.
Pipelining 3rd party apps¶
To be written.