Hi @Stefan and @Richard_Rodrigues1, I figured I’d QIIME-in on this.
I agree with Stefan’s very good and succinct responses. I would only like to emphasize the following:
If you have a reference tree (and the associated sequences) for your marker gene, then you are likely better off using the q2-fragment-insertion. Especially, if your reference phylogeny (and associated representative sequences) encompass neighboring relatives of which your sequences can be reliably inserted. Obviously, this is not always possible and constructing a de novo tree may be your only option and can be sufficient. Though in many cases, making use of a curated reference set in which to perform fragment insertion may be ideal.
Many factors can affect the reliability of a given phylogeny. But I’d like to highlight a few here:
- The alignment method (e.g. de novo or reference based) and alignment algorithm / parameters used.
- The length of the alignment and whether or not an alignment is masked. As Stefan pointed out, there is often less phylogenetic information from which to build a robust phylogeny from short sequences.Though this depends on the amount of informative sites and observed alignment patterns.
- The phylogenetic model under-which the phylogeny was constructed. Depending on the marker gene (region) used, this can also have large impacts on the overall resulting phylogeny. Being able to use or even test for appropriate substitution models may be limited by the tools used (e.g. some offer only one or a few models). In the worst case, even using an appropriate model may not even help as there is not enough sequence information to begin with!
For points 2 & 3, IQ-TREE has some recommendations for constructing “more reliable” phylogenies when confronted with building a de novo tree from very short reads. I’ve tried to outline some of that here. That being said, I generally agree with Stefan’s assessment. That is, using q2-fragment-insertion. But it does not hurt to also compare with the de novo approach. I hope I’ve helped to add a little insight.
-Best wishes on your 
building! 