[Bioperl-l] DNA distance methods [was Bio::Tools::Phylo::PAML with(baseml from PAML package)]

[Chris Fields]

> On Jun 24, 2006, at 11:05 PM, Ryan Golhar wrote:
> 
> >>> they make no assumption about coding sequence,
> >>> where do you get that impression
> >
> > I get that information from the 1.5 api docs:
> >
> > http://doc.bioperl.org/releases/bioperl-1.5.0-RC1/
> >
> great - I would also always point people to the LIVE code
> documentation not the 1.5.0-RC1 which is +1 years old, but nothing
> particular has changed in this module since 1.5.0 that I know of.
> Someday someone will put a new ball of docs up on the site, but I
> hope that will come with the next development or stable release.

Though I agree that the bioperl-live code is the best place for docs as it's
the most up-to-date, that fact isn't really emphasized much on the docs
page; the link is along with the other toolkits at the bottom of the page
and is listed as Bioperl Core Code (some users don't seem to get that, in
general, bioperl=bioperl core).  Could be this is causing a bit of confusion
for some.   The page hasn't really been updated in a while so that could
explain a lot; I'm not sure I can actually do any updating myself (or that I
should be able to!).  Maybe the best way to go is to have a wiki page for
this instead...(thinking aloud, sorry).

I was also thinking we should add something to http://doc.bioperl.org
indicating the age of the various docs as most are over 2 years old, or at
least link to the Release Pumpkin page which indicates the code release date
for the various releases:

http://www.bioperl.org/wiki/Release_pumpkin

Besides that, I agree with pretty much everything that you said; the
Bio::Align::DNAStatistics docs seem self-explanatory.

BTW, is the following still true (from Bio::Align::DNAStatistics):

"The routines are not well tested and do contain errors at this point.  Work
is underway to correct them, but do not expect this code to give you the
right answer currently!  Use dnadist/distmat in the PHLYIP or EMBOSS
packages to calculate the distances."

I'll likely be using this and Bio::Align::ProteinStatistics at some point
relatively soon myself so I may be up to some testing on one/both of these
modules if needed.

Chris

....