My understanding of IQtree is to start from a roughly good initial tree, and then run many iterations to sample different trees until they hopefully converge. In ncov, the IQtree parameter is -ninit 10 -n 4 -me 0.05 -nt AUTO -redo (here), and monkeypox seems to go with the augur tree default -ninit 2 -n 2 -me 0.05 -nt AUTO -redo (here). The number of iterations seems quite small but I also see that with larger trees, more iterations becomes very costly. Just want to check whether you guys have a good sense whether the small number of iterations is usually good enough and/or whether this is a parameter worth playing around with at all for SARS-CoV-2 and mpox trees. Thanks!