SH test

[Aderounmu Adedeji]

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]

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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