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. ______________________________________________________________________ ______________ Now that's room service! Choose from over 150,000 hotels -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: allbacteriafasta Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070320/ 7869a982/attachment.pl