Bootstrap value using ape package and including it in phylogenetic tree
0
0
Entering edit mode
@f4fcee4e
Last seen 3.1 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 • 2.7k views
ADD COMMENT
1
Entering edit mode

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
0
Entering edit mode

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

Login before adding your answer.

Traffic: 930 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6