[TNT] Colleague having problems saving node labels/tree tags to NEXUS format

[Jacqueline Silviria]

Good afternoon,

A colleague recently posted this on a Discord server, concerning exporting NEXUS or Newick files from TNT with node annotations:

I'm part of this collaboration that involves comparisons between RevBayes and TNT results, and any time these involve associating numeric values with nodes (branch indices, bootstrap support values, etc.), my collaborator will send me SVG or PDF images instead of actual tree files. This drives me insane, because I have to extract all that information manually, with my own eyeballs and fingertips, instead of doing it using ape or treeio [in R]...My collaborator admitted that if there is a way to export annotated tree files, he doesn't know how to do it. The thing is... he's not a TNT beginner…

I do not know the solution since I usually don’t use NEXUS files other than to upload them to Mesquite and convert them to TNT or PHYLIP. I’m forwarding the message to the group in case someone does.

Thanks,

Jacqueline S. Silviria
The Last King of the Jungle

Department of Earth & Space Science
University of Washington
Seattle, WA, USA
jsi...@uw.edu, sympan...@gmail.com

ResearchGate profile

Twitter: @JSilviria

Sent from my iPhone

[Santiago Catalano]

Hi Jacqueline,

You can do that using export - ;  . This command allows you to export the tree with the tags (annotations) on it. If you want to export the tree with resampling values, before running the procedure you need to turn on the tags (ttag=); then you run the resampling and after that you invoque the export - command. 

ttag =; 

resam  ; 

k 0 ; 

export -mytre.nex ; 

Bests,
Santi

  

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Dr. Santiago A. Catalano

Investigador Independiente CONICET

Unidad Ejecutora Lillo (UEL FML-CONICET)

FCNeIML-UNT

SM Tucumán - Tucumán
Argentina

Research Associate - Division of Anthropology at the American Museum of

Natural History. 

New York - USA 

[Santiago Catalano]

Hi Jacqueline,

have you solved the issue of exporting the tree labeled?

bests

Santi

On Fri, Apr 12, 2024 at 7:43 PM Jacqueline Silviria <sympan...@gmail.com> wrote:

--
Has recibido este mensaje porque estás suscrito al grupo "TNT-Tree Analysis using New Technology" de Grupos de Google.
Para cancelar la suscripción a este grupo y dejar de recibir sus mensajes, envía un correo electrónico a tnt-tree-analysis-using-n...@googlegroups.com.
Para ver esta conversación en el sitio web, visita https://groups.google.com/d/msgid/tnt-tree-analysis-using-new-technology/619CDC42-0DAA-4182-9BE1-8EA353E503E8%40gmail.com.