SH test

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Aderounmu Adedeji

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Sep 4, 2021, 4:27:38 AMSep 4
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Hello all, 

Is it possible to run likelihood tests like SH or KH tests in RAXML-NG. if not, what is the easiest way to run such analysis on a tree with ~ 900 taxa and 4000 amino acid sites. Thank you

Alexey Kozlov

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Sep 6, 2021, 9:49:24 AMSep 6
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Hi Aderounmu,

RAXML-NG can generate per-site log-likelihood scores:

raxml-ng --sitelh --msa ali.phy --tree best.tre --model GTR+G --prefix siteLH

which you can use as input for an external tool like CONSEL to perform SH/KH tests.

Alternatively, you can try IQTree, it implements many statistical tests, although AFAIK the
computation can be a bit slow on large datasets.

Best,
Alexey
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