proteinGTRmodel: meanings in the matrix

[Galya Klink]

Dear RAxML creators!

I'm sorry if my question has already been discussed here but I didn't find any information about meanings of numbers in cells of substitution matrix which RAxML gives me in a *model* site when I use it to reconstruct a phylogeny. Can you explain me please what do they mean exactly?

Many thanks!

Galya 

[Alexey Kozlov]

Dear Galya,

in RAxML_proteinGTRmodel.* file you have the AA substitution matrix itself (400 individual substitution rates between
all AA pairs, in first 20 lines) and equilibrium frequencies (20 values in the last line).

I guess the confusing part here might be the AA ordering, so please find it below (copy-pasted from RAxML code):

{'A','R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H','I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V'};

This order is used for both substitution matrix rows/columns and for the frequencies.

Hope this helps,
Alexey

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[Heiko]

{'A','R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H','I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V'};

Just a side-note: This order might look confusing, but it is just the alphabetical order of the full names of the amino acids ;)

Cheers,
Heiko

[Alexey Kozlov]

thanks Heiko, that's good to know! :)