[Bioperl-l] Bug? Phyml parameters

[Jason Stajich]

Probably best to submit it as a bug to redmine (redmine.open-bio.org) 
especially as for your first request is more of a feature request -- if 
you are comfortable with coding you can make changes and submit a pull 
request via git when you've made changes.

As for the second one, I can fix that right away, but it is helpful to 
have a bug report so we can track things that are in progress so things 
don't slip through the cracks.

Generally speaking I use RAXML or GARLI for my ML trees but hopefully 
there are users with PHYML interests too.

Adam Retchless wrote:
> Dear BioPerl crew,
>
> I noticed some strange behavior in how the Phyml wrapper treats 
> parameters, and am wondering if there is a reason for this, or if it 
> is a bug.
>
> Documentation is here:
> http://doc.bioperl.org/bioperl-run/lib/Bio/Tools/Run/Phylo/Phyml.html
>
> Being new to BioPerl, I'm not exactly sure what is the right way to 
> address this. Let me know if this should just be reported as a bug 
> rather than writing to the list...
>
> 1) The major issue is that the wrapper seems to disable the option to 
> calculate confidence values for the trees (e.g. bootstrap, aLRT). In 
> the documentation, I see no option to set this parameter, and the 
> "_setparams" subroutine has a comment line explicitly stating "no 
> bootstrap sets" 
> (http://doc.bioperl.org/bioperl-run/lib/Bio/Tools/Run/Phylo/Phyml.html#CODE26).
>
> A web search revealed no discussion of this point. In fact, there were 
> several references to the bootstrap values arising from Phyml, making 
> me think that it used to be enabled (or there is some other way to 
> enable it).
>
> 2) While digging into the above issue, I looked at the "new" 
> subroutine and it looks like the "freq" parameter is mis-assigned. The 
> value of "freq" is given to the variable $kappa rather than $freq. 
> (Code here: 
> http://doc.bioperl.org/bioperl-run/lib/Bio/Tools/Run/Phylo/Phyml.html#CODE1)
>
> Any information on this (particularly #1) would be appreciated.
>
> Thanks,
> Adam
>
>

-- 
Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki