partitioning with IQTREE

[Rohit Rannavre]

Hello guys,

I am a newbie to IQTREE and writing to seek your help with the same. I am trying to set a model for each partition with the following command:  

iqtree2.exe -s DatasetAligned.phy -p partitions.nex -m TESTMERGE -merit BIC -B 1000 -bnni -T AUTO

My codon-based partitions file (partitions.nex) looks like this:

#nexus
begin sets;
     charset p1 = 1-1695\3;
     charset p2 = 2-1695\3;
     charset p3 = 3-1695\3;
end;

In return, I am getting just one model for the three partitions. Is there anything wrong or is it the way IQTREE works?

Your inputs on this issue will be much appreciated and thank you in advance.

[Rob Lanfear]

Hi Rohit,

For help with IQ-TREE, please use the IQ-TREE github discussions.

Yours,

Rob