Error viewing trees using FigTree

[Farah Aidil Fitri]

Hi there, 

I am a beginner in using TNT. I have problem with viewing my trees using FigTree through by TNT formatted data. It keeps on telling me "Error reading tree file: Missing closing ')' in tree". However, I tried viewing the same data I analyzed using PAUP. And it can be viewed. 

I tried analyzing morphological data, with 100 characters, 30 taxa. I run the search using the traditional search method, with: 

1. Wagner trees 1000 replicates

2. Swapping algorithm : TBR with 10 trees to save

Memories are hold at 10 000.

After running the command, it showed an SPR algorithm with 1000 replicates instead of TBR. 

(I have attached pictures comparing mine and my friend's command, it's the same using the above parameters but the results are different).

I have tried re-creating the nexus file through Mesquite and exporting it to TNT format, but it was no use.

I also have tried running my friend's data (morphological data; 134 characters; 28 taxa), using the same parameters and commands, and it can be viewed by FigTree. 

The only difference is the TBR / SPR search. 

I would appreciate it if anyone could clarify the problems as I have Googled everything and could not understand what is wrong or how to resolve it.

Many thanks. 

[Santiago Catalano]

Hi Farah, 

use the command export:

export = Farah.tre ; 

bests,

Santiago

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Dr. Santiago A. Catalano

Investigador Adjunto CONICET

Unidad Ejecutora Lillo (UEL FML-CONICET)

FCNeIML-UNT
SM Tucumán - Tucumán
Argentina

[Farah Aidil Fitri]

Hi there, this is the command I used.

hold 10000 ;  

log 70_run_log ;  

taxname = ;  

mult=replic 1000 tbr;

collapse-;

bbreak = tbr ;  

stats.run

nelsen * ;  

tchoose { strict } ;  

ttags = ; 

blength *;  

ttags );

export - consensus_70.tre ; 

ttags -;

ttags = ;  

collapse tbr ;  

resample sym replications 1000 ;  

resample boot replications 1000; 

resample jak replications 1000; 

keep 1 ;  

ttags );  

export - allsample.tre;

proc/;