Beginner's Question: Rooting Phylogenies to proceed with IQ2MC workflow

[walkyshitake]

Hello,

I am running IQTREE v3.0.1 Windows with proteins sequences from a gene family of interest. My command line was:
iqtree3.exe -s seq.fasta.

My goal is to construct an ultrametric tree based on the maximum likelihood tree output from IQTREE and estimate the divergence time using MCMCtree.
I am aware that the command I mentioned will only construct an unrooted tree, which I need to check on root phylogenies directory for a next-step guidance. I am uncertain how to obtain a NEXUS partition file. Should I use the command:
iqtree3 -p FOLDER_NAME --out-aln OUTFILE_NAME
to generate it?

I would greatly appreciate any guidance or clarification on this matter. Thank you for your time and assistance.