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

Ryan Golhar golharam at umdnj.edu
Sun Jun 25 13:20:12 EDT 2006

Exactly.  Also on the page it says (in the descriptionfor

In order to use these methods there are
several pre-requisites for the alignment.

   DNA alignment must be based on protein alignment. Use the subroutine
aa_to_dna_aln    in Bio::Align::Utilities to achieve this.

 Etc etc etc

The rest of the pre-reqs also mention that the sequences should be
coding sequences.  Because of this, I thought DNAStatistics was only for
coding sequences and could not be used for non-coding sequences...

Anyway, I've gotten past my troubles and am on to finish this project.
I think the isssues I ran into others might run into as well.  I'd be
happy to contribue what I can but need to finish this stuff first...
Thanks for all your help Jason, Chris, Sendu!


-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu] 
Sent: Sunday, June 25, 2006 1:06 PM
To: 'Jason Stajich'; golharam at umdnj.edu
Cc: bioperl-l at lists.open-bio.org
Subject: RE: [Bioperl-l] DNA distance methods [was
Bio::Tools::Phylo::PAML with(baseml from PAML package)]

> 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:


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.



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