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HyPhy: Hypothesis testing using Phylogenies
http://www.hyphy.org
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Difference between --reference-group and --reference flag (RELAX) #1616

Closed liamfriar closed 1 year ago

liamfriar commented 1 year ago

Hi, I was receiving the same prompt to choose my test and reference groups as @stephenshank screenshotted in #1446 . I am trying to build an automated pipeline, so this would not work well. I found that adding the --reference-group flag fixed the problem, but I am now confused what the difference is between --reference-group and --reference ? My current call seems to work, but I want to make sure I am not doing something different than I intend? I see that there is a "Group test mode" option when I call hyphy relax --help but I can't figure out what that is, so maybe it is related?

hyphy relax --alignment mod.${alignment_file} --tree $out_tree --reference-group "Background" --test "Foreground" --reference "Background" --models Minimal
rm *tmp

Originally posted by @liamfriar in https://github.com/veg/hyphy/issues/1446#issuecomment-1570652782

spond commented 1 year ago

Dear @liamfriar,

--reference-group only makes sense when you run RELAX in group mode (available if you have >2 sets of branches), triggered by --mode "Group mode". Otherwise, use --reference Name.

Best, Sergei