\
>>> 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).
See Controlling BLAST.
To be written.
To be written.
To be written.
To be written.