iqtree2 -nt 10 -s input.fa -m GTR2+FO+I+R10 -alrt 1000 -bb 1000 -asr --mlrate -wslmr -wspmr
Refer run_iqtree.sh script for more details.
Refer set_outgroup.py script for more details.
Refer iqtree_internal_state_table_to_sequence.py script for more details.