[Biopython-dev] Phylip interface questions

Peter biopython at maubp.freeserve.co.uk
Mon Jul 27 19:43:09 UTC 2009

On Mon, Jul 27, 2009 at 7:42 PM, Marshall Hampton<mhampton at d.umn.edu> wrote:
> Thanks Peter, I was unaware of the EMBOSS versions of PHYLIP.  I don't
> think using pexpect to wrap the originals is really that hard - I have some
> working fine already - but now I see its almost pointless. I don't like the
> EMBOSS dependence, but it sounds like you are already working on
> getting rid of that.

I'm not quite sure what you are saying. Biopython doesn't depend on
EMBOSS, we just have some optional code to interact with EMBOSS.

If you want to run the PHYLIP tools from Python, you are going to have to
install PHYLIP or EMBOSS anyway. The EMBOSS version is (I think) far
more useful, and there is lots of other useful stuff in EMBOSS as well,
so I really don't see a problem with recommending EMBOSS.

Right now we have parsers and wrappers for some of the EMBOSS
tools, and I would like to have more. Generating the wrappers (semi)
automatically would be a step forward as we currently have wrappers
for only about ten of the EMBOSS tools (hand picked based on people
actually wanting to use them from within Biopython).


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