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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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Ascertainment Bias Correction #15

Closed esteinig closed 7 years ago

esteinig commented 7 years ago

Thanks you so much for this amazing re-write, very much looking forward to using it. Is there any chance to implement the ascertainment bias correction options from RAxML?

amkozlov commented 7 years ago

Ascertainment bias correction is already available as of version 0.4.0.

You can use same models as in old good RAxML, namely:

Lewis: e.g.--model GTR+G+ASC_LEWIS

Felsenstein: e.g. --model GTR+G+ASC_FELS{1000} // 1000 invariant sites

Stamatakis: e.g. --model GTR+G+ASC_STAM{1000/2000/3000/4000} // 1000 invariant As, 2000 Cs, 3000 Gs, 4000 Ts

See also: https://github.com/amkozlov/raxml-ng/wiki/Input-data#evolutionary-model

Please let me know if there will be any problems/questions.

esteinig commented 7 years ago

My apologies for overlooking the Wiki entry - this is exactly it. Many thanks!

amkozlov commented 7 years ago

Great, so I will close this issue now.