Re: [raxml] "ERROR: Bootstrap tree #1 has wrong number of tips"

[Alexandros Stamatakis]

Maybe in one of the two tools some duplicate/identical sequences were
removed automatically? Might be good to check the respective logs for
warnings.

Did you double-check that you used the same input MSA in both cases?

Alexis

On 22.08.24 17:32, Kenta Renard wrote:
> Hello,
>
> I am trying to apply branch supports using a set of bootstrap trees to
> an ML tree. I get the "ERROR: Bootstrap tree #1 has wrong number of
> tips" error when there are the same number of tips in the ML tree and
> the bootstrap trees. What could be going wrong here? The ML tree was
> inferred in IQ-TREE but I have not had this problem before. I can send
> files if needed.
>
> Best,
> Kenta
>
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--
Alexandros (Alexis) Stamatakis

ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.biocomp.gr (Crete lab)
www.exelixis-lab.org (Heidelberg lab)

[Kenta Renard]

Dear Alexis,

The ML tree was generated from what was originally a PHYLIP file with cut the taxon IDs but I could not change this output. Additionally, the MSA itself was different (I wanted to see how a different MSA of the same sequences affected calculated branch supports).The other file for the bootstrap trees was a fasta file. I thought I could account for the truncated taxon IDs in the ML tree by removing the same number of characters in the fasta file (and this removed any warnings about identical IDs). But then when I tried to run again, I got the error mentioned in the first post.

Best,

Kenta 

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[Oleksiy Kozlov]

Dear Kenta,

please post your input files (trees) and full raxml-ng logs file, then you will save us a lot of
guesswork :)

Thanks,
Oleksiy

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>
> --
> Alexandros (Alexis) Stamatakis
>
> ERA Chair, Institute of Computer Science, Foundation for Research and
> Technology - Hellas
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
>

> www.biocomp.gr <http://www.biocomp.gr>       (Crete lab)
> www.exelixis-lab.org <http://www.exelixis-lab.org> (Heidelberg lab)

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