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

[Jason Stajich]

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:

    JukesCantor
    Uncorrected
    F81
    Kimura
    Tamura
    F84 (Felsenstien 84)
    TajimaNei
    JinNei


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
--
Jason Stajich
jason at bioperl.org
http://jason.open-bio.org/