Hi,

I am trying to re-draw a tree from the GA-Branch output because the output seems to collapse everything into a polytomy (though I gave a tree that shows the relationships).  I have attached a file that has two re-drawn trees based off of the GA-branch outputs on the second page.  I have colored an internal branch that is missing from the GA-Branch output in gray (meaning there is no value), but I'm not sure if this is the correct way to do it.  Should the gray branch be the same as the other branch that splits from this node ? In general, how do we interpret these internal branches when they are collapsed in the output?  Thanks for your help!

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Hi JB,

1). GABranch uses time-reversible models, hence the placement of the root is indeterminate. HyPhy automatically "unroots" rooted trees, because that's what the analysis is run on.

2). GABranch has been deprecated in favor of BranchSiteREL (also available on datamonkey). Essentially, GABranch does not allow site to site rate variation (only branch to branch), but BranchSiteREL can do both. The result is considerably more power.

Sergei