IQTree model testing by locus and first, second and third codon posiiton

[Stefan Dahl]

Hi,

I'm a current Master's student and not very experienced with IQTree. I'm trying to run model testing on my data partitioned by locus as well as by first, second, and third codon position.

The output file only seems to have one model for each locus, rather than selecting models for all three codon positions throughout the alignment.

Can someone help me figure out what I'm missing?

Thanks,

Stefan Dahl

[Mark Miller]

Hi Stefan,

Can you paste the contents of the file _JOBINFO.TXT from a job run into a reply?

This will help me locate the job run you are referring to.

SIncerely,
Mark Miller

[Stefan Dahl]

Hi Mark,

Thanks for getting back to me. File output:

Task\ label=IQTree-model-selection-commandline
Task\ ID=3330043
Tool=IQTREE_XSEDE
created\ on=2026-04-20 00:21:02.0
JobHandle=NGBW-JOB-IQTREE_XSEDE-947C3427C66743F79CE4EEED54C6307C
RunNumber=1
resource=expanse
User\ ID=148062
User\ Name=stefan_dahl
email=stefa...@student.adelaide.edu.au
Output=(results,*,UNKNOWN,UNKNOWN,UNKNOWN)
ChargeFactor=1.000000
cores=128
JOBID=48233073

Thanks,

Stefan

[Miller, Mark]

Hi Stefan,

I regret to say that this question is a bit out of my level of understanding of IQ Tree.

I would recommend you contact the IQ Tree folks directly, or try their AI chat tool.

https://iqtree.github.io/

Sorry I could not be more helpful.

Mark

---

From: cipres-science...@googlegroups.com <cipres-science...@googlegroups.com> on behalf of Stefan Dahl <stefa...@gmail.com>
Sent: Tuesday, April 21, 2026 3:48 AM
To: CIPRES Science Gateway Users <cipres-science...@googlegroups.com>
Subject: Re: IQTree model testing by locus and first, second and third codon posiiton

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