\

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# 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
              \0.678---|
                       |          /-HowlerMon
                        \0.720---|
                                  \-Human

And if you have matplotlib installed you can draw the tree (see Drawing dendrograms and saving to PDF).

### 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.

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