Question: Verifying Phylogeny Trees
gravatar for Jamand
10.0 years ago by
European Union
Jamand110 wrote:

Hi all

I've build a phylogenetic tree using Phyml (ML method), but some branches have low bootstrap values and so seemed not to be confirmed. How can I fix it?

Best regards

phylogenetics tree • 6.0k views
ADD COMMENTlink modified 2.1 years ago by Biostar ♦♦ 20 • written 10.0 years ago by Jamand110
gravatar for Neilfws
10.0 years ago by
Sydney, Australia
Neilfws49k wrote:

"Fix it" is not really the correct way to think about this.

Bootstrapping is a statistical method, used to get around the problem that you have imperfect data (i.e. not as many sequences as you would like). Typically, the way it works is to generate a "fake" sequence based on the real sequences, add it to the alignment and see whether sequences still cluster on the same branch. You repeat that an arbitrary number of times (perhaps 100 or 1000) and count the proportion of times that you got the same branch.

Low values mean lower confidence. You may be able to improve the scores using better data, such as more real sequences or better optimization of the alignment. However, it's important to realise that these are statistical methods and they do not really give "right" or "wrong" answers. Rather, you should think of the statistic as telling you something about your data.

ADD COMMENTlink written 10.0 years ago by Neilfws49k

An early (the first?) paper describing the application of the bootstrap to phylogenetics, by Felsenstein, gives a great introduction to the topic, I find. You might like to look at that for help understanding what's going on here (Felsenstein, 1985, Evolution, 39, 783-91, Confidence limits on phylogenies: an approach using the bootstrap.)

ADD REPLYlink written 7.9 years ago by aidan-budd1.9k
gravatar for Lars Juhl Jensen
10.0 years ago by
Copenhagen, Denmark
Lars Juhl Jensen11k wrote:

Like Neil eluded to, the way to "fix" low bootstrap values is to improve the data based on which the tree is constructed. Here are a few things that you may consider doing:

  1. If you are building a species tree, you should strongly consider basing it on multiple genes using either concatenated alignments or super-tree methods.
  2. Poor support for a given branch pattern may be due to poor species coverage in that part of the tree. Including additional genes that diverged around the same point in the tree may improve your resolution and hence bootstrap values.
  3. Bootstrap values (and trees in general) can be badly affected by alignment errors. Using a better multiple alignment program, improving the alignment with refinement programs such as RASCAL, manually checking the alignment, and eliminating the less confident parts of your alignment (e.g. with GBlocks) can thus all improve your results.
ADD COMMENTlink written 10.0 years ago by Lars Juhl Jensen11k
gravatar for aidan-budd
7.9 years ago by
aidan-budd1.9k wrote:

One way of addressing part of this "problem" uses the concept of "rogue" taxa (see Wilkinson M. 1996. Majority-rule reduced consensus trees and their use in bootstrapping. Mol. Biol. Evol. 13: 437–444.), taxa which are found in different "positions" in different trees (e.g. the trees estimated from different bootstrapped replicates of your alignment dataset.

By removing/pruning these taxa from your analysis, you can often see a gratifying "improvement" in the support values for for other branches.

Andre and Denis, working with Alexis Stamantakis in Heidelberg, just published a webservice that can be used to help identifying such taxa, that you might like to take a look at

obviously, if the taxa you're most interested in working with are identified as rogues, you're going to need to think carefully about your analysis!

ADD COMMENTlink written 7.9 years ago by aidan-budd1.9k
gravatar for Larry_Parnell
10.0 years ago by
Boston, MA USA
Larry_Parnell16k wrote:

Very good answers from neilfws and Lars Juhl Jensen. I'll add just a minor point that rooting the tree and changing the root can also have an effect on the relationships of other taxa to themselves. In other words, your problematic area(s) may look different if you change or add an outgroup to root the tree. I prefer to use more than one outgroup when doing this. For example, if I'm building a tree with primate sequences, I may through in a dog and bovine, maybe cat sequences as well so that my outgroup can also form a branching pattern.

ADD COMMENTlink written 10.0 years ago by Larry_Parnell16k
gravatar for Yo_O
9.7 years ago by
Yo_O130 wrote:


you can cutoff your low bootstrap values if you want to with this webservice :

Your input have to be a Newick file.

Best regards.

ADD COMMENTlink written 9.7 years ago by Yo_O130
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