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.