[BioC] problems in boot.phylo()

[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:

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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