amkozlov/raxml-ng

Substitution rates

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liamxg commented

Dear @amkozlov,

What is the Substitution rates for each value?

Substitution rates (ML): 0.077246 0.706620 0.177535 0.293354 2.188834 1.000000

liamxg commented

And what is the rates?
weights&rates: (0.250000,0.000000) (0.250000,0.000000) (0.250000,0.000001) (0.250000,3.999999)

amkozlov commented

The rates define upper triangle of the substitution matrix, e.g. for GTR the order is A-C, A-G, A-T, C-G, C-T, G-T.

Please see here for more details:
https://github.com/amkozlov/raxml-ng/wiki/Input-data#evolutionary-model

liamxg commented

Thanks.