My lab mates and I unable to conduct an SH test in RAxML on CIPRES. We have used a .phy file for our input, deselected "Configure Bootstrapping," supplied our best tree in a .tre file from our previous run using the same .phy file under "Simple Parameters', selected "Compute a log likelihood test," supplied our "Bootstrap_Result" file. Did we miss a step/is there a better way to do this?
I think the SH test in RAxML need two trees, and I'm not sure if it can compare a best tree with the bootstrap trees in this way. In the command line would be something like this raxmlHPC.exe -f h -t ref -z trees - s alg -m GTRGAMMA -n TEST. As it not estimate the trees again (just optimizes the lk for the trees) is a fast analysis to run even on a laptop (if your alignment is not enormous)
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