Bootstrap values on newick tree
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7.7 years ago
ddowlin ▴ 70

Hi all,

I have a newick format tree with about 70 sequences. I created the tree with 1000 bootstraps. However when I visualise the file (e.g. FigTree, Geneious) I get 1001 separate trees with no option to view the bootstrap values on the consensus tree.

Is there a way I can "merge" the 1001 trees into a single consensus tree with bootstrap values?

Thanks in advance.

phylogenetics tree bootstraps newick • 4.9k views
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7.7 years ago
kloetzl ★ 1.1k

That is what phylip consense is for.

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7.7 years ago
Joe 21k

What did you make them with?

RAXML has a whole separate function to add bootstrap values from bootstrap trees on to the main result tree. Can't remember all the details off hand but it's on their wiki/documentation

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They were made with PhyML.

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7.4 years ago
Joseph Hughes ★ 3.0k

If you are using the right PhyML command you should have a file _phyml_tree.txt which provides you with the bootstraps on the maximum likelihood tree.

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