[BioC] problems in boot.phylo function

[Nora Muda]

Dear BioConducter useRs,
 
I have problems in writing boot.phylo() function. 
 
Let say I have 30 aligned sequences; then I computed
pairwise distances with "K80" method. Then I construct
phylogenetic tree with neighbor-joining method and my
proposed method. Now I have problems in writing "FUN"
in boot.phylo() function. Below are examples of my
programs:
 
library(ape)
allbacteria <- read.dna("allbacteriafasta","fasta")
distallbacteria <-
dist.dna(allbacteria,pairwise.deletion=TRUE,as.matrix=TRUE)
plot(nj(distallbacteria))
 
boot.phylo(plot(nj(distallbacteria)),allbacteria,nj(distallbacteria))
 
What should I put as FUN in boot.phylo?
 
I make comparison between distances of "K80" in PHYLIP
and dist.dna("K80").There are a lot of differences esp
in PHYLIP there is a default for
transversion/transition rate; which is 2 but not in
ape package. How to modify it to make it the same?
 
Hope you all may help. Your attention are really
appreciated.
 
 
Regards,
Nora.



 
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