Dendroscope failed to open the IC/ICA tree file

[Black Jungle]

Here is it.

I calculated a IC/ICA tree, however, there are "[" in file text, how can I open this tree in picture?

Thanks

[Alexandros Stamatakis]

Did you post-process the RAxML outpout file with some other tool (e.g.
FigTree) before reading it with Dendroscope?

There is evidently something wrong with the tree file.

Alexis

On 27.04.23 11:32, Black Jungle wrote:
>
> Here is it.
> I calculated a IC/ICA tree, however, there are "[" in file text, how can
> I open this tree in picture?
>
> Thanks

> 微信截图_20230427162945.png
>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com>.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/raxml/bff937f2-efe6-4667-9ceb-ac80d536c050n%40googlegroups.com <https://groups.google.com/d/msgid/raxml/bff937f2-efe6-4667-9ceb-ac80d536c050n%40googlegroups.com?utm_medium=email&utm_source=footer>.

--
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)

[Lucas Czech]

Hi there,

the bracket "[" starts a comment in the newick file format, see https://doi.org/10.1093/molbev/msx055, and hence is valid. As far as I am aware, Dendroscope should be able to handle such comments.

From the picture that you shared, it seems to be a valid file - assuming that the single quotation marks are put there by Dendroscope, and are not part of the file itself. That is, the '0.07...[0.406' string. If those single quotation marks are in the file, then that's broken. If not though, it might be that the number is too long for Dendroscope to parse, or some other bug, in which case this is a bug in Dendroscope, which you then should report to the developer.

Hope that helps,
Lucas

[Lucas Czech]

Hi again,

update on that: incidentally, I also tried Dendroscope now with a similarly annotated file, and it failed with the same error that you saw. Hence, this is an issue in Dendroscope: it should ignore the content within brackets, as those are newick comments, but doesn't. I'd recommend getting in touch with the developers there.

Cheers
Lucas

[Black Jungle]

Thank you for your answering. Is there any other software suggested to open the result filetxt? 

Yours,

Gengshen

[Lucas Czech]

Hey Gengshen,

I think iTOL (http://itol.embl.de/ ) can handle this, and even show the annotations in those brackets.

Alternatively, you can use the gappa command `clean-tree` (https://github.com/lczech/gappa/wiki/Subcommand:-clean-tree) to remove those. Then, you should be able to view the tree with Dendroscope or other tree viewers as well, but without the content in brackets. For the `clean-tree` command, you want to use at least the `--remove-comments-and-nhx` flag.

Cheers
Lucas

To unsubscribe from this group and stop receiving emails from it, send an email to raxml+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/raxml/3a21d8c3-1188-45bb-8f5f-aaf3ce1e1169n%40googlegroups.com.