How to implement heterozygote sites in IQ-TREE?

[SYSU-SinLee]

Dear developers，

Thanks for your efforts to develop and maintain the software.

I've read the manual, tutorial and some debates in the user group. It is quite clear for me that the way IQ-TREE dealing with ambiguous sites, but how can I implement heterozygote sites for phylogeny analysis in IQ-TREE? By Raxml-ng, I can just keep these sites, encode them with IUPAC and use GENOTYPE model, is there a similar model in IQ-TREE?

Thanks for your time and wait for your reply.

Best regards, Li Sen

[tseemann]

Thje documentation for v1.6 says it does handle IUPAC codes correcrtly. So I assume 2.x is the same.

[SYSU-SinLee]

Thje documentation for v1.6 says it does handle IUPAC codes correcrtly. So I assume 2.x is the same.

Thanks for your reply. I think there are some differences between "ambiguous sites" and "heterozygous sites". "Ambiguous" refers to an unknown status, which means on this site there is either "A" or "T". While the "heterozygous" is a certain status with both "A" and "T". They should be treated in different ways. I don't know if this make me clear. If you have any suggestions or opinions on this, please let me know. Thanks a lot.