Thanks a lot for your help! I just have a couple more questions/clarifications.
First, I actually have 4 gene trees, with 7 partitions. 4 of the partitions are all mitochondrial and hence share the same tree, and the same clock model. I have them partitioned by codon position, plus a noncoding partition, to allow for separate site models. But anyway, it sounds like 4 threads is the correct number.
Second, I'm unsure of how estimating substitution rates fits into what you've described. I want to account for the differences between the mtdna codon partitions, and estimating substitution rates seems like the way to do that, but will that cause a non-identifiability issue if I then also give the mtdna gene tree its own clock rate?
Third, by default "automatic set clock rate" and "automatic fix mean substitution rate flag" are deselected; do these have any role to play in Starbeast 3?
And fourth, when you say to give the species tree an informed time-calibrated rate, would that involve fixing this rate or estimating it and setting an appropriate prior?
I apologize for having so many questions; I felt I had a good grasp of the substitution and clock rate situation with regular BEAST2 and Starbeast, but adding in the species tree clock is throwing me for a curve.