[Biopython-dev] pypaml

[Peter Cock]

On Fri, Jun 10, 2011 at 12:09 PM, Brandon Invergo <b.invergo at gmail.com> wrote:
> On Fri, Jun 10, 2011 at 12:58 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> Adding C code has drawbacks as it has to compile on multiple
>> platforms, and cannot be used in Jython (and likely not in IronPython
>> or PyPy - I've not kept up to date with their progress). Also, it doesn't
>> see a good use of time to reimplement something the next version
>> of PAML will include.
>>
>> I would wait for the next version of Chi2.
>
> Ok that makes sense. I'll remove chi2.py from the module (though if
> people still want it, it'll still be over at my pypaml.googlecode.com
> page). I'll keep my eye on his page for new versions.

OK

> I also just now decided that I'm going to change all of the default
> control file option values. At the moment, they're set to the values
> found in example files when you download the PAML package. However
> these don't necessarily reflect the most common values. I just see it
> being a source of confusion and or problems in the future (ie people
> not realizing that an option is set to a value that will negatively
> affect their results). Better to set all the values to None and let
> the user decide what are the best values.

That sounds best.

Peter