for name, seq in known_sequences.items():
f.write(">"+str(name)+"\n")
f.write(seq+"\n")
### Align
if verbose: print "aligning..."
aln_file_name = os.path.splitext(temp_file_name)[0] + ".afa"
align_muscle(temp_file_name, aln_file_name, gapopen=-1000.0)
### Build tree
if verbose: print "building tree..."
tree, aln = build_tree_FT(aln_file_name)
### Show in pretty format
pretty_tree = PhyloTree(str(tree), alignment=aln_file_name, alg_format="fasta")
pretty_tree.ladderize()
ts = TreeStyle()
pretty_tree.render(outfile, tree_style=ts)
### Clean up your mess
os.remove(temp_file_name)
os.remove(aln_file_name)
### TODO
# highlight adapter rows
# root on adapter?
# tweak alignment parameters so it's better
# understand muscle alignment score. how can we rationally change parameters to improve?
