Visualizing annotated newick output?

[cjpardodelahoz]

Hi,

What software do you use for visualizing the annotated newick tree that QuartetScores produces as the output? I've tried FigTree and I get "Number format error: For input string : "0.0463378[qp-ic", which is is the branch length and annotation of the first bipartition that shows up in the output file. I also have not been able to parse the annotations inside the square brackets into R with neither ape nor treeio functions. I attach one of my trees that were annotated with QuartetScores. Thank you for your help and this useful tool! quartet_scores_95.txt

[zhouxiaofan1983]

Dear Carlos,

You can try DendroScope (http://dendroscope.org/).

Best, Xiaofan

On Sat, Dec 24, 2022 at 2:47 AM Carlos J. Pardo De la Hoz < @.***> wrote:

Hi,

What software do you use for visualizing the annotated newick tree that QuartetScores produces as the output? I've tried FigTree and I get "Number format error: For input string : "0.0463378[qp-ic", which is is the branch length and annotation of the first bipartition that shows up in the output file. I also have not been able to parse the annotations inside the square brackets into R with neither ape nor treeio functions. I attach one of my trees that were annotated with QuartetScores. Thank you for your help and this useful tool! quartet_scores_95.txt https://github.com/lutteropp/QuartetScores/files/10296875/quartet_scores_95.txt

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[cjpardodelahoz]

Thank you for the suggestion. I tried dendroscope and got a similar error when opening the file: "Expected number at position 103, instead got '0.0463378[qp-ic'"

[zhouxiaofan1983]

Hi Clarlos,

Please used the attached perl script to reformat the output of QuartetScores (e.g., perl reformat_quartetscores_output.pl quartet_scores_95.txt > quartet_scores_95.new.txt). The IC scores will be displayed as nodal support values together with the original support (which will be the last number in the new tree). Please let me know if this works for you.

Best, Xiaofan

On Tue, Dec 27, 2022 at 12:12 AM Carlos J. Pardo De la Hoz < @.***> wrote:

Thank you for the suggestion. I tried dendroscope and got a similar error when opening the file: "Expected number at position 103, instead got '0.0463378[qp-ic'"

— Reply to this email directly, view it on GitHub https://github.com/lutteropp/QuartetScores/issues/8#issuecomment-1365269295, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZE6STNE2TBKEW3KE5IA7DWPG7VXANCNFSM6AAAAAATH7O2VA . You are receiving this because you commented.Message ID: @.***>

[lczech]

Hi @cjpardodelahoz,

on the topic of phylogenetic tree visualization tools, I'd also highly recommend to have a look at this article, which explains why tools have trouble with certain newick variants, and has some tips and caveats for working with the format that might help you here.

Hope that helps, cheers Lucas

[cjpardodelahoz]

Hi Xiaofan,

Could you please re-attach the script? Somehow I cannot see a link to download it. Thank you!

Carlos

[jungleblack007]

Hi Carlos and Xiaofan, I met the same problem, and hadnot found the reformat_quartetscores_output.pl script. Where should I get it? Thank you!

Gengshen

[lczech]

Hi @zhouxiaofan1983,

are you receiving notifications for this repository? I don't have the script that people are missing here - could you please help?

@jungleblack007 and @cjpardodelahoz, sorry that you did not get an answer yet - if Xiaofan does not get notifications here, I recommend reaching out via email instead ;-)

Cheers Lucas

[Xiaojun928]

Hi @zhouxiaofan1983,

could you please reattach the reformat_quartetscores_output.pl script? we cannot find the link to download it. Thanks a lot!

Cheers, Xiaojun

[zhouxiaofan1983]

Sorry guys, just saw the messages from this repository. I have re-attached the script, please let me know if you have any problem accessing or using it.

Best, Xiaofan reformat_quartetscores_output.zip

[Xiaojun928]

Many thanks for your help!