[BioC] boot.phylo( ) function

[Earl F. Glynn]

I am looking for a similar solution using only R/Bioconductor packages. 
After not finding any examples of using boot.phylo from Google, I sent a 
note to the author of boot.phylo asking if any working examples are 
available.  Perhaps Emmanuel Paradis can join this discussion.

I have used the PHYLIP programs "neighbor" and "consense" for this, and used 
R to create the files for "neighbor".  I can now put these working notes 
online to give some idea about using neighbor and consense: 
http://research.stowers-institute.org/efg/Report/BootstrapTree.pdf   (since 
the related paper was published late last year).  While these notes are 
quite specific to our particular problem, they show how R can be used to 
create distance matrices for input to PHYLIP's "neighbor" program. A 
complete solution in R is desirable, but I haven't found one yet.

I'm hoping boot.phylo can do something similar, but the documentation needs 
to have some better examples so the software can be used.

efg
Earl F. Glynn
Scientific Programmer
Bioinformatics
Stowers Institute for Medical Research


"Nora Muda" <noramuda at yahoo.com> wrote in 
message news:855563.43819.qm at web61024.mail.yahoo.com...
> Dear BioConducter useRs,
>
> I have problems in writing boot.phylo() function.