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.