I am working with a poorly defined genus of fungi with very few publicly available genomes and I am wanting to cluster the all available ones plus my novel ones into putative species. I am unsure of a good workflow for this.

Would it be better to current phylogenetic workflows of multiple sequence alignment and tree construction and then based on some phylogenetic distance threshold cluster the genomes into species?

OR

Would some form of multiple sequence analysis (with Busco datasets for example) or core genome analysis (with Roary) where we take SNP differences between the MLSA sequences or core genomes and then based on a SNP count threshold cluster the assemblies into putative species?

I apologies if this is a naive question but any help would be appreciated.
I don't think there is a "best" approach in your situation, given 

1) the taxonomy of the group is probably still flaky.

2) being draft genomes, they probably are spotty and have sizeable gaps, and maybe even contaminants. Repeat regions are often left out of such assemblies.

Actually, a good workflow would perform different types of analyses, in order to get a more complete and solid overall picture about the genus. Some suggestions:

[ReferenceSeeker][1] will give you the closest species, in terms of kmer (min-hash) distances and average nucleotide identity (ANI). You can easily find if there are some really close genomes with it.

[Mashtree][2] uses the same kmer (min-hash) distances to group genomes in a dendrogram. The authors don't consider this dendrogram a phylogeny, but I think this dendrogram probably reflects the phylogenetic history of the genomes, anyway. Thus, it may complement a more traditional core genome phylogeny. Whole genome alignments probably aren't a good option, unless all genomes are really close (and, I would argue, also really high quality). Mashtree works as a substitute for whole genome alignments.

A core genome phylogeny would complement the above analyses (but I don't think [Roary works][3] for fungal genomes). As there aren't many genomes available, you can get a SNP-based phylogeny, or even a maximum-likelihood or Bayesian phylogeny with all genes concatenated. Running the same version of BUSCO on all genomes would also give a good dataset for a phylogeny, in addition to informing on the overall quality of the genomes.


  [1]: https://github.com/oschwengers/referenceseeker
  [2]: https://github.com/lskatz/mashtree
  [3]: https://github.com/sanger-pathogens/Roary/issues/425