This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Bootstrap values on newick tree

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
• 6,264 views • link
updated by Joseph Hughes Joseph Hughes • written by ddowlin ddowlin

3 answers

That is what phylip consense is for.

• 0 views • link
written by kloetzl kloetzl

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

• 0 views • link
written by Joe Joe

They were made with PhyML.

• 0 views • link
written by ddowlin ddowlin

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.

• 0 views • link
written by Joseph Hughes Joseph Hughes

Log in to answer this question.

More posts like this