[Bioperl-l] Bug? Phyml parameters

[Adam Retchless]

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


-- 

Adam Retchless
Center for Genomic Sciences
Allegheny-Singer Research Institute