FixedTreeAnalysis error for Import Tree

[Tiago Simoes]

Hi all,

I am using BEAST 2.7.5, and I want to use a fixed tree for my analyses. I decided to use the FixedTreeAnalysis package, but while I use the Import Tree option to load my Newick tree, I get an error message saying that it could not find any trees in the file. This happens for trees with and without branch lengths included....

....And yes, I have triple checked it is actually in Newick format, and it happens for other tree files as well. Is anyone getting similar issues?

Cheers,

[Omar Mejía]

You can do it in Beauti and desactivate the operators to force a topology, I can share the instructions but until Monday, let me know

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[higg...@gmail.com]

Hi Tiago,

Can you try with tree in NEXUS format instead of Newick?

Cheers,

Remco

[dco...@rsabg.org]

Hi Omar,

Can you still share the instructions or what operators you used to force a topology ?

Thanks,

Dylan

[­Wonseop Lim]

Hi Dylan, 

I hope this link helps: https://www.beast2.org/fix-starting-tree/

and if you are using Optimized Relaxed Clock, https://groups.google.com/g/beast-users/c/jIvejETqhXw/m/qyTmTAmoBAAJ

2024년 7월 9일 화요일 오전 4시 17분 58초 UTC+9에 dco...@rsabg.org님이 작성:

[Omar Mejía]

Dear Dylan:

I have attached the instructions on how to deal with forcing a tree topology in Beast:

You need to attach the newick tree into Beauti and generate the xml file as usual, after it,   you need to  remove (delete ) the four operators for tree proposal moves: Subtree-Slide, Narrow Exchange, Wide Exchange, and Wilson-Balding in wordpad or similar, save as xml and run Beast



    <operator id="YuleModelSubtreeSlide.t:tree" spec="SubtreeSlide" tree="@Tree.t:tree" weight="15.0"/>

    <operator id="YuleModelNarrow.t:tree" spec="Exchange" tree="@Tree.t:tree" weight="15.0"/>

    <operator id="YuleModelWide.t:tree" spec="Exchange" isNarrow="false" tree="@Tree.t:tree" weight="3.0"/>

    <operator id="YuleModelWilsonBalding.t:tree" spec="WilsonBalding" tree="@Tree.t:tree" weight="3.0"

Note: You need to take some cautions with your newick inputfile:

1) The input tree must contain distances, and cannot be only Newick format

2) Check that the number of OTUs in your Nexus and tree files are the same

3) Check that the names in the tree and in the Nexus inputfile are identical

4) Force the tree to be ultrametric, rooted and binary in library ape

is.binary
is.rooted
is. ultrametric

6)Export the tree in R

7) Import the tree to Beauti and save the xml

8) Open the xml file and desactivate the operators

9) Run Beast

Have fun

Let me know if it works

Best regards

Omar

Libre de virus.www.avast.com

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Omar Mejía G