Re: How to map bootstrap support values onto a consensus tree?

[Camilo Mattoni]

Hi Gregory,

You can save trees in nexus format (with commas) on TNT using the command "export - newfile.nex". Only the trees in memmory will be saved. If you want the matrix and the trees, use "export * newfile.nex".

Hope this help.

Cheers,

Camilo

 

El 01/12/12 15:32, gpenn escribió:

I finally figured out how to save bootstrap support values onto a consensus tree using the command line version of tnt. Here's how it worked, note that there is still a problem with the trees, which I have to fix using sed.

1) load matrix and consensus tree (as tree 0).

2) tnt*> tsave* consensus_bootstrapped.tre;

3) tnt*> ttags=;

4) tnt*> taxname=;

5) tnt*> resample boot frequency replications 100000;

6) tnt*> save *;

7) tnt*> tsave /;

I'm still having trouble with TNT not using commas in its parenthetic tree format. In order to use another application, like Archaepoteryx or TreeGraph 2 to view trees created by TNT, I have to use sed to fix the formatting by inserting commas where appropriate. Does anyone know how to fix this in TNT?

Cheers,

Gregory

On Thursday, November 29, 2012 9:43:20 AM UTC-7, gpenn wrote:

I forgot to mention in my original post that I am using the command line version of TNT. This is probably relevant.

On Thursday, November 29, 2012 9:43:20 AM UTC-7, gpenn wrote:

I forgot to mention in my original post that I am using the command line version of TNT. This is probably relevant.

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