[Biopython-dev] pypaml

Brandon Invergo b.invergo at gmail.com
Fri Jun 10 16:11:19 UTC 2011

On Fri, Jun 10, 2011 at 5:59 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
> If you've already ported the code to pure Python or Python+Numpy/Scipy, do
> you think it would make sense to provide this function under
> Bio.Phylo._utils instead of in your PAML module? Then users would be able to
> do a likelihood ratio test on trees without having the PAML binaries
> installed.

That would be fine by me. I guess there's not much sense in getting
rid of it entirely since it's already been written.

> The pure-Python version would still be handy for smaller degrees of freedom,
> and if someone happens to be using PyPy it would probably be wicked fast.
> The best solution is probably Numpy, rather than Scipy, since other parts of
> Biopython already use Numpy as an optional dependency.

I don't think Numpy has a Chi^2 cumulative distribution function; you
can only draw random numbers from the distribution. Scipy has that,
but as a user, I would be annoyed to have to install a huge package
just to perform likelihood ratio tests. I like the idea of having it
built into biopython, since I think it's a fairly common procedure
given all the maximum likelihood techniques in biology. That's just my
2 cents though...


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