Biopython PRANK Alignment

Question

[catarina.tserrano]

Hi!

Does someone used PRANK in a Biopython script? I cannot understand the parameters used.

I tried this one, but no file with alignments was generated.

>>> from Bio.Align.Applications import PrankCommandline
>>> prank_cline = PrankCommandline(d="unaligned.fasta",
...                                o="aligned", # prefix only!
...                                f=8, # FASTA output
...                                notree=True, noxml=True)

[st.ph.n]

You have the command, but did you run it? Add another line with prank_cline()