Question

Bootstrap value using ape package and including it in phylogenetic tree

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Lanjamarina • 0

@f4fcee4e

Last seen 3.2 years ago

Madagascar

Dear bioconductor users,

I have problems in having the bootstrap value from the boot.phylo() function. I actually have DNA sequences from SANGER sequencer of ITS4 region). I read the user guide of ape package and any kinds of helps that bring me to the following codes:

dna<-fasta2DNAbin("ITS4.fas")
dna<-read.dna("ITS4.fas", "fasta")
D<-dist.dna(dna, model = "F84")
tree<-nj(D)
tree<-ladderize(tree)
myBoots<-boot.phylo(tree, dna,function(dna) tree)
ape::plot.phylo(tree, align.tip.label = T, cex = 1, x.lim = 0.3)
nodelabels(myBoots, adj = 0.7, cex=0.7, frame = "none", col = "red")

I expected to have bootstrap values in my phylogenetic tree but instead of that I got the default number of bootstrap replicates in each node.

Phylogenetics • 2.8k views

ADD COMMENT • link 3.3 years ago Lanjamarina • 0

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Hi, can you please elaborate further on what is the problem by showing a screenshot? Can you please also check the contents of your objects by using the str() function? For example, please try str(myBoots)

ADD REPLY • link 3.3 years ago Kevin Blighe ★ 4.0k

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Hi, thank you for your request. Recently "myBoots" gave me something like this:

> myBoots
 [1]   NA 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000
[18] 1000 1000 1000 1000 1000
>

That's the way I thought that these were the number of bootstrap replicates.Then I change the line code of boot.phylo(tree, dna, B=1000, function(dna) tree) to boot.phylo(tree, dna, B=1000, FUN=function(dna) nj(D)). Actually, it is appearing something like this:

> str(myBoots)
 int [1:22] NA 0 0 0 0 3 0 7 0 40 ...
> myBoots
 [1] NA  0  0  0  0  3  0  7  0 40  0  0  0  0  1  0 24  1  2 27 27 32

Then I don't understand what is it. I wonder to have a bootstrap like 80% or just 80 or something that might be usefull

ADD REPLY • link 3.3 years ago Lanjamarina • 0