How To Add 1000 Bootstrap value in Phylogenetic Tree From Binary Data Getting From RAPD and ISSR Analysis

I have binary data of 19 species of plants amplified by RAPD and ISSR molecular markers. I constructed a phylogenetic tree by using ape and phangorn packages in R-software. I need to add a 1000 bootstrap values on previously constructed phylogenetic tree. Please help me regarding this. I will be really obliged.

phylogeny phangorn bootstrap

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written 4.5 years ago by Seemab •

I have edited the tags. That way you will likely get help faster than by stating the urgency of the matter.

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written 4.5 years ago by Michael Dondrup

1 answer

Please check the documentation carefully: https://cran.r-project.org/web/packages/phangorn/phangorn.pdf The phangorn package has a function called bootstrap.pml

Or use another software like Iqtree if you have problems doing this in R.

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written 4.5 years ago by Michael Dondrup

Thanks for the suggestion.

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written 4.5 years ago by Seemab •

well In my case, Two RAPD primers were amplified for 19 Species and were manually genotyped binary data (0,1). I have no sequential data. I used the following script to construct the phylogenetic tree: library(ape) library(phangorn) ntaxa <- 19 nchar <- ntaxa - 15 tree <- rtree(ntaxa, br = NULL)

Gets descendants, but removes the first ntaxa elements,

which are the individual tips

char_mat <- array(0, dim = c(ntaxa, nchar))

RAPD <-data.frame(RAPD_OPD16_08_) for (i in 1:nchar) { RAPD_OPD16_08_[,i] <- replace(RAPD[,i], y <- desc[[i]], 1) } Error in replace(RAPD[, i], y <- desc[[i]], 1) : object 'desc' not found now I found error here.

rownames(RAPD) <- tree$tip.label RAPD plot(tree)

Also, I need similarity matrix table and want to add bootstrap values in this tree. Please help me regarding this matter

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written 4.5 years ago by Seemab •