Hi Antony,
ascertainment bias correction is now available in RAXML-NG v0.4.0:
https://github.com/amkozlov/raxml-ng/releases/tag/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
Please let me know if there will be any problems/questions.
Best,
Alexey
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