Question: Performing fast bootstrap in R using ape package
20 months ago by
User000 • 270
User000 • 270 wrote:
I would like to perform a nj tree with 1000 bootstrap on my snp data. I have around 5K snps and I am using R package ape:
snp <- as.matrix(objt) stree = nj(dist.gene(snp)) myBoots <- boot.phylo(stree, snp, function(xx) nj(dist.gene(xx)), B = 1000, mc.cores = 6)
It has been 3 days so far it is still running, any suggestion how to make it faster, if it is possible at all.
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