Hello all,

I am trying to create a phylogenetic tree using DECIPHER and the phagorn package in R for 16s amplicon data. However, it is taking too much time, Any other alternatives to create a phylogenetic tree?

The commands used to construct phylogenetic tree after assigning taxonomy are as follows:

sequences<-getSequences(seqtab.nochim)
names(sequences)<-sequences
alignment <- AlignSeqs(DNAStringSet(sequences), anchor=NA)
phang.align <- phyDat(as(alignment, "matrix"), type="DNA")
dm <- dist.ml(phang.align)
treeNJ <- NJ(dm)
fit = pml(treeNJ, data=phang.align)
fitGTR <- update(fit, k=4, inv=0.2)
fitGTR <- optim.pml(fitGTR, model="GTR", optInv=TRUE, optGamma=TRUE,
                    rearrangement = "stochastic", control = pml.control(trace = 0))

Any help would be appreciated.