set candidate models frewuencies to e and f?

[Alejandro Manzano]

I am trying to run a model test and set it to test both e and f frequencies. However, I when i am setting '-f ef' (following the same logic as setting -h igfr), I am getting in the log

  include model parameters:
    Uniform:         false
    p-inv (+I):      true
    gamma (+G):      true
    both (+I+G):     true
    free rates (+R): true
    fixed freqs:     true
    estimated freqs: false

Am I correct in assuming it is only turning on fixed frequencies? It certainly looks that way from the output.

Thanks

[Diego Darriba]

Hi Alejandro,

With "-f ef" both fixed and estimated frequencies should be "true" as you mentioned. However, this is also the default behavior if you do not set the "-f" argument. Which modeltest version and OS are you using? I have not seen this error before.

Best,

Diego.

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[Kenta Renard]

Dear Diego,

I have the same issue. I cloned the Github repository and whether I use the MPI or multithreads version the issues persists.

Best,

Kenta