Bootstrap values on newick tree

Question

[ddowlin]

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.

Answer 1

[kloetzl]

That is what phylip consense is for.

Answer 2

[Joe]

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

[ddowlin]

They were made with PhyML.

Answer 3

[Joseph Hughes]

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.