List of all modules allowed with correct syntax

Alessandra Aleotti

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Dec 12, 2023, 2:55:05 AM12/12/23

to GeneRax

Hello!

I was wondering if there is anywhere a list of all the substitution models that GeneRax recognizes and their correct syntax for the family file? I am looking for some of the newer substitution models like the Q.pfam - is this available for GeneRax and if so with which syntax?

Many thanks!

Best regards,

Alessandra

Benoit Morel

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Dec 12, 2023, 3:51:01 AM12/12/23

to Alessandra Aleotti, GeneRax

Hi Alessandra,

Yes, we support the models that raxml-ng supports. You can find the corresponding documentation here: https://github.com/amkozlov/raxml-ng/wiki/Input-data#evolutionary-model

If any of these models does not work, do not hesitate to contact me.

Best,

Benoit

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Alessandra Aleotti

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Dec 12, 2023, 4:03:54 AM12/12/23

to Benoit Morel, GeneRax

Hi Benoit,

Thanks a lot, that's exactly what I was looking for!

Best,

Alessandra

Athulya Girish Kizhakke

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Feb 24, 2026, 3:56:27 AMFeb 24

to GeneRax

Q.mammal and Q.bird were returning errors for me, at least with GeneRax v2.0.4 (says "Cannot read alignment file (file exists but is invalid)" but works fine when I use LG instead.)