Question: Bootstrap values on a phylogenetic tree (RAxML).
gravatar for vasilislenis
4.6 years ago by
United Kingdom
vasilislenis100 wrote:

Hello everybody,

I am trying to construct a phylogenetic tree by using RAxML software.

These are my fist tries, so my knowledge is a little bit limited.

I run the following command:


raxmlHPC-SSE3 –f i -s all_sheep_mt.phylip -n boot -m GTRGAMMA -b 12345 -p 123456 -# 1000

and RAxML generated the file with all the 1000 trees (RAxML_bootstrap. boot).

I also run the previous command without the -b parameter and I took each tree on a different file and a file with the best one (RAxML_bestTree.boot).

finally, I run the following command in order to have except the branch lengths and the the bootstrap values (percentage of confidence).

raxmlHPC-SSE3 –f b -m GTRGAMMA -s all_sheep_mt.phylip -z RAxML_bootstrap.boot -t RAxML_bestTree.boot -n   bootTree

The problem is that I finally have only the branch lengths onto the tree.

Any idea what I'm doing wrong?


Thank you very much in advance,



ADD COMMENTlink modified 4.6 years ago by Brice Sarver3.2k • written 4.6 years ago by vasilislenis100
gravatar for Brice Sarver
4.6 years ago by
Brice Sarver3.2k
United States
Brice Sarver3.2k wrote:

You seem to have the general approach right. Without looking at your data, I'll throw out a couple suggestions.

1) I don't think that you need to supply your sequence data when you use -f b. This just needs the tree to annotate and the replicates. I don't know why this would screw things up.

2) When you make consensus trees, you get a couple trees where the confidence values are placed on the branches on one and the nodes on the other. If you attempt to visualize the tree with, say, FigTree, the program will complain if you provide the wrong one. It might be the case that your tree is actually annotated, but the program you are using to visualize it is screwing up. Are you getting both types of trees?

The RAxML manual, specifically under "Obtaining Confidence Values," might be of help here. I also like to do the all-in-one ML and bootstrapping approach, and this might make things easier if you feel comfortable doing so with your data.

ADD COMMENTlink written 4.6 years ago by Brice Sarver3.2k

Thank you very much for your answer. Yes, the existence of the alignment file in the -f b stage was the reason.

I followed the manual more careful and finally I did it. I have two trees with the support values as you said, one can be opened with FigTree, the other (with the braces for the nodes) not. Now I'm facing a more serious problem, the values are quite low, but I believe that I have to make a new question for this. It's not the first time that you are helping me and I'm really grateful for that :)

ADD REPLYlink written 4.6 years ago by vasilislenis100


I want to display the bootstrap values in RAxML tree. Can you please mention the code which u had used?

ADD REPLYlink written 2.5 years ago by jiffyjohn230
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