Hi guys! I'm analysing fungal DNA sequences (ITS) obtained from MySeq platform, and I'm trying to build a phylogenetic tree for beta diversity analysis. I used PIPITS to process my raw data and then I aligned the sequences using MUSCLE, then filtered them and I'm going to use qiime for making phylogenetic tree. My question is if I have to specify in the instruction:

make_phylogeny.py -i alignedseqs.fasta -r midpoint -o rooted_rep_set.tre

that i want to construct the tree with de muscle method or if it is okay to use the default method that in this case is fasttree:

-t TREE_METHOD, --tree_method=TREE_METHOD Method for tree building. Valid choices are: clustalw, raxml_v730, muscle, fasttree, clearcut [default: fasttree] Thank you!