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lutteropp / QuartetScores

Code for computing various support scores for internodes
GNU General Public License v3.0
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Visualizing annotated newick output? #8

Open cjpardodelahoz opened 1 year ago

cjpardodelahoz commented 1 year ago

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 commented 1 year ago

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

— Reply to this email directly, view it on GitHub https://github.com/lutteropp/QuartetScores/issues/8, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZE6SWAG7KYVQE3HJUFQ5TWOXXU3ANCNFSM6AAAAAATH7O2VA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

cjpardodelahoz commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

Hi Xiaofan,

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

Carlos

jungleblack007 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

Many thanks for your help!