Question

solution of boot.phylo()'s problem

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Nora Muda ▴ 70

@nora-muda-2065

Last seen 10.2 years ago

Thank you to Martin and Earl for their response and answered. I got answered from Emmanuel Paradis. Below are the solutions: 'boot.phylo(phy,x,FUN,B=100,block=1)' x is a character matrix (not the distance matrix) that will be resampled for the bootstrap. My mistake is not to store the tree which is needed by boot.phylo; so tr <- nj(distallbacteria) Therefore; boot.phylo(tr,allbacteria,FUN=function(xx)nj(dist.dna(xx,pairwise.dele tion=TRUE) We also can refer to the book on using R for phylogenetic analyses, written by Emmanuel Paradis : http://www.springer.com/west/home/statistics/stats+life+sci?SGWID=4-10 134-22-156993712-0 --Nora. ______________________________________________________________________ ______________ TV dinner still cooling? Check out "Tonight's Picks" on Yahoo! TV.

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ADD COMMENT • link updated 14 months ago by Trinh • 0 • written 17.7 years ago by Nora Muda ▴ 70

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Dear Nora, I have a similar problem.

protein_seq <- readAAStringSet("./protein_seq.fasta")
msa <- msa(gene_seq, method = "Muscle")

msa_aln <- msaConvert(gene_seq, type="seqinr::alignment")

d <- dist.alignment(msa_aln, "identity")
tree <- nj(d)

bp <- boot.phylo(tree, msa, function(xx) 
  nj(dist.alignment(xx, "identity")))

I tried different inputs for the parameter x of boot.phylo (raw seq, msa object), but they did not work. Could you please give me an example of x's structure? Thank you very much for your help

ADD REPLY • link 14 months ago Trinh • 0