FixedTreeAnalysis with a known discrete trait value at the root

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Stephen Staklinski Jr.

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Jan 30, 2024, 12:21:56 PMJan 30
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I can run the FixedTreeAnalysis for my data with a fixed tree for which I input discrete trait labels for the tips of the tree. Is it possible to also specify the discrete trait value as fixed at the root if it is known?

Remco Bouckaert

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Jan 30, 2024, 1:35:51 PMJan 30
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Hi Stephen,

What you can do is add a zero branch length taxon to the root and give it the desired value.
Just edit the Newick like so: if the fixed tree looks something like 

((A:1.0,B:1.0):1.0,C:1.0)

wrap it in brackets, and add taxon R with branch lengths zero:

(((A:1.0,B:1.0):1.0,C:1.0):0.0,R:0.0)

Taxon R should show up in the list of taxa where you can give it the root value.


An alternative is to set up root frequencies through the rootFrequencies input of the tree likelihoods, but that requires editing of the XML.

Cheers,

Remco

On 31/01/2024, at 6:13 AM, Stephen Staklinski Jr. <steph...@gmail.com> wrote:

I can run the FixedTreeAnalysis for my data with a fixed tree for which I input discrete trait labels for the tips of the tree. Is it possible to also specify the discrete trait value as fixed at the root if it is known?

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Stephen Staklinski Jr.

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Jan 30, 2024, 5:04:07 PMJan 30
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Thank you, this worked well.
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