RAxML NG : custom amino acid substitution model

[Thomas Ed. Bigot]

Hi,

Is it possible with raxml-ng to use a custom amino-acid model?

I’d like to specify a transition matrix (in paml format for instance), like one can do with paml (http://www.iqtree.org/doc/Substitution-Models#protein-models § User-defined empirical protein models

)

Thanks in advance,

Thomas

[Alexey Kozlov]

Hi Thomas,

yes it is possible, although the format is slightly different:

https://github.com/amkozlov/raxml-ng/wiki/Input-data#single-model

e.g. something like "--model PROTGTR{rates.txt}+FU{freqs.txt}" - please
note that rates are in different order (upper triangle)!

PAML format support is on my TODO list however, and it will become
available in the next release I guess.

Best,
Alexey

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[Thomas Ed. Bigot]

Thanks a lot for your reply.

For protein model, what order is expected? Is it, as for PAML, alphabetical order of three letter aminoacid codes (“Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val”) or the alphabetical order of IUPAC one letter code ?

Thank in advance,
Thomas

[Alexey Kozlov]

Hi Thomas,

aminoacids are in the following order:

https://github.com/amkozlov/raxml-ng/wiki/Input-data#defaults

Best,
Alexey

[Thomas Ed. Bigot]

So I can notice it matches the alphabetical order of three letter codes, like in Paml.

Thanks !

Cheers,

Thomas

Le mardi 19 février 2019 17:57:26 UTC+1, Thomas Ed. Bigot a écrit :

[Alexey Kozlov]

yes, I guess that's how this particular order came about...

Alexey