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

Jason Stajich jason at bioperl.org
Sun Jun 25 08:37:11 EDT 2006

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.

> Its documented under the description section.
i don't really see what you refer to since there is a lot of  
documentation, but perhaps it should be clarified - I had hoped this  
was a sufficient description:
"This object contains routines for calculating various statistics and  
distances for DNA alignments."

> Oh well, I have it coded and working...might as well use it.
Sounds like your best bet for your situation.

For the record and in the mailing list archives - as long as you  
don't call a method that contains "KaKs" it will work fine.  You can  
calculate distances using the currently implemented distance methods:

    F84 (Felsenstien 84)

It will be more productive is to just drop the discussion since you  
seem to be fine without all of this anyways  - if you decide you  
would like to use it and contribute new distances methods or doc  
fixes I am sure we'll enjoy your contributions.

Jason Stajich
jason at bioperl.org

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