Hello everyone. I need to build a phylogenetic tree using IQ-TREE, starting from a sequence alignment in CODON format of several invertebrates. These are my charsets:

nexus

BEGIN SETS;

charset atp6.fasta = 1-651;
charset atp8.fasta = 652-729;
charset cob.fasta = 730-1749;
charset cox1.fasta = 1750-3237;
charset cox2.fasta = 3238-3858;
charset cox3.fasta = 3859-4632;
charset nad1.fasta = 4633-5484;
charset nad2.fasta = 5485-6156;
charset nad3.fasta = 6157-6459;
charset nad4.fasta = 6460-7683;
charset nad4L.fasta = 7684-7899;
charset nad5.fasta = 7900-9294;
charset nad6.fasta = 9295-9663;

END;

I would need to remove the third bases, how should I write them? These are the commands with which I would launch IQ-TREE:

iqtree -s "fasta_file" -bb 1000 -alrt 1000 -m MFP+MERGE -spp "charset.nexus" -st CODON5

Please, any suggestions would be very helpful.