Getting snippy-core results ready for IQTree

[alanxelena]

Hi!

I have a question regarding how to treat the snippy-core results to feed them into IQTree afterwards. So right now, I have the core.full.aln file, should I first go for the snp-sites and then snippy-clean or the other way round? Another question, according to a thread in which Torsten participated (https://bitsandbugs.org/2019/11/06/two-easy-ways-to-run-iq-tree-with-the-correct-number-of-constant-sites/) The best approach to use IQTree on SNP data should be to use the -fconst function but I'm a little confused by this, in the thread Torsten mentions a pretty straightforward method:

iqtree -fconst $(snp-sites -C core.full.aln) -s <(snp-sites -c core.full.aln)

In this case, do I need to select a nucleotide substitution model (for example with -m TEST)? Or will this overrun the -fconst option?

Thank you very much!