Question: Bootstrap values on newick tree
0
gravatar for ddowlin
2.7 years ago by
ddowlin70
ddowlin70 wrote:

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.

ADD COMMENTlink modified 2.4 years ago by Joseph Hughes2.7k • written 2.7 years ago by ddowlin70
1
gravatar for kloetzl
2.7 years ago by
kloetzl1.0k
European Union
kloetzl1.0k wrote:

That is what phylip consense is for.

ADD COMMENTlink written 2.7 years ago by kloetzl1.0k
0
gravatar for jrj.healey
2.7 years ago by
jrj.healey12k
United Kingdom
jrj.healey12k wrote:

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

ADD COMMENTlink written 2.7 years ago by jrj.healey12k

They were made with PhyML.

ADD REPLYlink written 2.7 years ago by ddowlin70
0
gravatar for Joseph Hughes
2.4 years ago by
Joseph Hughes2.7k
Scotland, UK
Joseph Hughes2.7k wrote:

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.

ADD COMMENTlink written 2.4 years ago by Joseph Hughes2.7k
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