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amkozlov / raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible
GNU Affero General Public License v3.0
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Substitution rates #182

Closed liamxg closed 1 month ago

liamxg commented 1 month ago

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 1 month ago

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 1 month ago

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 1 month ago

Thanks.