iqtree3 "site-freq" option: name clash in the context of AliSim and Mixture models under PMSF

[danieltamarit]

Dear iqtree team,

It seems that iqtree3 (3.0.1) has two parameter settings called by "--site-freq":

• site frequency model file (for reconstructions using mixture models)
• site frequency mimic mode (for alignment simulation with AliSim)

Currently, the latter masks the former. For example, the following command:

iqtree3 -m LG+C10+G4 -s test_quick.fa -pre test_quick.fa.PMSF_LGC10G4_sftest --site-freq test_quick.fa.PMSF_LGC10G4.sitefreq

produces the following error:

Use --site-freq MEAN/SAMPLING/MODEL

However, using the older "-fs" equivalent to the mixture-model "--site-freq" parameter does run:

iqtree3 -m LG+C10+G4 -s test_quick.fa -pre test_quick.fa.PMSF_LGC10G4_sftest -fs test_quick.fa.PMSF_LGC10G4.sitefreq

For completeness, I have used the attached test alignment and ".sitefreq" file, generated via the commands:

iqtree3 -m LG+C10+G4 -s test_quick.fa -pre test_quick.fa.LGC10G4
iqtree3 -m LG+C10+G4 -s test_quick.fa -pre test_quick.fa.PMSF_LGC10G4 --tree-freq test_quick.fa.LGC10G4.treefile -n 0

Files here:
files.zip

I hope this helps. Please let me know if I missed something, though.

Thanks so much for all your work. Big fan.

Best,
Daniel