Hey all!
I'm running a phylogenetic analysis on the output of a snippy-core run using IQTree. As far as I understood it's important to consider the invariant sites for this type of data by either performing the analysis + ASC of using the -fconst option. From this thread: https://bitsandbugs.org/2019/11/06/two-easy-ways-to-run-iq-tree-with-the-correct-number-of-constant-sites/ I understand that the best approach it to go for the -fconst option. My doubt now is the following: should I ask IQTree to perform an model test (-m TEST) and then give the -fconst parameters or will the selection of the model overrun the latter? I have posted this question in the IQTree Github page but got no reply, any previous experience or help will be greatly appreciated.
