Dear,

I work on 16S pacbio dataset. I used DADA2 to get my taxonomy, and now I would like to use raxml-ng to get a phylogeny. I first ran DECIPHER to get my sequences alignment and it goes well :

./raxml-ng --check --msa ./output/alignment.fasta --model GTR+G

(...)
[00:00:00] Reading alignment from file:./output/alignment.fasta
[00:00:00] Loaded alignment with 18299 taxa and 10649 sites

Alignment comprises 1 partitions and 10649 sites

Partition 0: noname
Model: GTR+FO+G4m
Alignment sites: 10649
Gaps: 86.32 %
Invariant sites: 45.54 %

Alignment can be successfully read by RAxML-NG.

It is a very time-consuming to get my boostraped tree, using :

./raxml-ng --all --msa ./output/alignment.fasta --model GTR+G --prefix test --seed 2 --threads 128 --bs-metric fbp,tbe

That's why I try to go by first, get a consensus tree from 100 trees and then, compute the bootstrap values :

#consensus
./raxml-ng --msa ./output/alignment.fasta --model GTR+G --prefix test --tree pars{50},rand{50} --threads 128 --start

./raxml-ng --consense MRE --prefix consensus  --tree test.raxml.startTree --threads 128 

#bootstrap 
./raxml-ng --msa ./output/alignment.fasta --model GTR+G --prefix T7 --seed 2 --threads 128  --bootstrap

The bootstrap step is still runing. I will use the --support option to map these values on the tree if it ends on time.

Is it a correct way to do?

Best