Why no bootstrap value for tree built by IQTREE

[Xinxin Zhu]

Thank you

I have a puzzle, I can't find bootstrap value in result files after run IQTREE. So how to obtain the BS value in IQTREE?  Thank you for providing help me.

[Minh Bui]

Hi Xinxin,

We can’t really help here without detailed information. Please at least provide a command line, IQ-TREE version used. Did you use ultrafast (-bb option) or standard bootstrap (-b option)?

Minh

On 18 Jul 2021, at 5:32 pm, Xinxin Zhu <xinxin...@gmail.com> wrote:

Thank you

I have a puzzle, I can't find bootstrap value in result files after run IQTREE. So how to obtain the BS value in IQTREE?  Thank you for providing help me.

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[Xinxin Zhu]

Dear professor

Thank you very much. I don't know which value represents the Bootstrap value in the final tree file. After I finished the modelFinder,  I again conducted the command including -bb, it told me there was existed the bootstrap value result, but I can't find which files contain it. In the picture, I don't know which value is bootstrap value, 3.089? if the 3.089 is bootstrap value, it seems incorrect.

Thank you very much.

[Heiko Schmidt]

Dear Xinxin,

The problem is that there are different values or labels that can be shown inside a tree - besides bootstrap of ufboot values.


Which tool did you use to visualise the tree?

If you use FigTree, it will detect that there are some values annotated in the tree, and it asks what these annotations are suggesting a label for it (called “label” by default).

If one wants to, one can change the label to something more meaningful like “ufboot”.

Next if you switch on branch labels or node labels in the navigation bar on the left, FigTree will show the branch lengths (or tree heights - I can’t remember) by default.

However, you have the choice to change this in the branch/node labe setup to “label” or however you renamed this to.


Just from the values, I guess, then figure currently shows the branch lengths at the branches and the heights at the nodes (because they seem to increase by the branch lengths from the leafs towards the root).

I hope this is helpful,
Heiko

> On 26.07.2021, at 08:52, Xinxin Zhu <xinxin...@gmail.com> wrote:
>
> Dear professor
>
> Thank you very much. I don't know which value represents the Bootstrap value in the final tree file. After I finished the modelFinder, I again conducted the command including -bb, it told me there was existed the bootstrap value result, but I can't find which files contain it. In the picture, I don't know which value is bootstrap value, 3.089? if the 3.089 is bootstrap value, it seems incorrect.
>
> Thank you very much.

> <1627282178(1).jpg>
> On Friday, July 23, 2021 at 6:39:59 AM UTC+8 Minh Bui wrote:
> Hi Xinxin,
>
> We can’t really help here without detailed information. Please at least provide a command line, IQ-TREE version used. Did you use ultrafast (-bb option) or standard bootstrap (-b option)?
>
> Minh
>
>
>> On 18 Jul 2021, at 5:32 pm, Xinxin Zhu <xinxin...@gmail.com> wrote:
>>
>> Thank you
>>
>> I have a puzzle, I can't find bootstrap value in result files after run IQTREE. So how to obtain the BS value in IQTREE? Thank you for providing help me.
>>
>>
>>
>> --
>> You received this message because you are subscribed to the Google Groups "IQ-TREE" group.
>> To unsubscribe from this group and stop receiving emails from it, send an email to iqtree+un...@googlegroups.com.
>> To view this discussion on the web visit https://groups.google.com/d/msgid/iqtree/175272bd-3932-4997-b651-16b0c5c77d68n%40googlegroups.com.
>
>
> --
> You received this message because you are subscribed to the Google Groups "IQ-TREE" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to iqtree+un...@googlegroups.com.

> To view this discussion on the web visit https://groups.google.com/d/msgid/iqtree/f36904fb-2aee-4c2c-8e85-652ba216ea9en%40googlegroups.com.
> <1627282178(1).jpg>

-----------------------------------------------------------------------------
Heiko Schmidt
Center for Integrative Bioinformatics Vienna (CIBIV)
University of Vienna / Max Perutz Labs
http://www.cibiv.at/
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[Xinxin Zhu]

Thank you very much

I try this method. but it seems not bootstrap value in treefile, right?  So I want to ask a question, where are the ufboot values?  The ufboot values do exist in the treefile,  only I used incorrect way incurring I do not see the ufboot value?   Thank you very much.

[Heiko Schmidt]

Dear Xinxin,

If you correctly started the IQ-TREE analysis with the -b (for standard bootstrap) or -bb (for UFboot), then there should be support values in the treefile.

Could you please send me your log file and your treefile directly to my email address (not into the google group forum).

Then I can take a look. With the current very little amount of information I have about your analysis I can only guess and speculate.

Best wishes,
Heiko

> To view this discussion on the web visit https://groups.google.com/d/msgid/iqtree/7d45187a-9503-4279-a4f0-e454cea02fben%40googlegroups.com.

-----------------------------------------------------------------------------
Heiko Schmidt
Center for Integrative Bioinformatics Vienna (CIBIV)
University of Vienna / Max Perutz Labs

Campus Vienna Biocenter 5 (VBC5)
A-1030 Vienna, Austria
-----------------------------------------------------------------------------
Email: heiko.schmidt(AT)univie.ac.at
Tel. : ++43 +1 / 4277 - 74321
http://www.cibiv.at/
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[Xinxin Zhu]

Thank you very much

    I will send your email when I finish the latest IQtree task.  Thank you very much for your help.