need some help on TNT and tree issues

[sfde...@yahoo.com]

Hi,

 

Version: Windows, TnT 1.1 (no taxon limit) May 2013.

 

I was trying today with a fasta file. I did exactly this sequence

 

Launch TNT

cdir C:\.. Directory path

nstates 32

procedure &Mystus_Annotated.fas

 

The file is read properly.

 

Now I choose

Settings -> Implied Weighting

Top Box "Search Trees" - I chose 'using implied weights'

Bottom Box " Weighting function" - I chose first button 'weight with default

function' K=3.0000

I click ok.

From top menu, I chose Analyze -> Estimate Consensu

Top box, Precision = 3

Next box, Accuracy = 4

I click OK

 

I get a tree, I press escape key to come back to TNT window.

Now, From top menu, I chose Tree -> View, I can see the tree.

To switch to command line mode, I toggle the view option.

 

I try to save the tree with these two options

 

export -trial.nex

export trial2.nex

 

With the minus option, it tells me "no tree to save"

without the minus optoin, it tells me "cannot export data with more than 10 states"

 

Now back to nstate command in the beginning:

 

If I try nstates 16, 8 etc. I get error while loading with

'procedure &filename'

The error is "Found alien symbol for taxon 0, char 4.”

The screen shot  (Attached) shows the complete session. After the blue horizontal bar, I show attempts with nstate 8.

Thank you so much for any help.

Sincerely,

Shobnom Ferdous

[Ângelo P. Pinto]

Dear Shobnom,

I do no understood exactly your question, but you said that have trees in the TNT memory... You will need specify a tree file and after send a tree(s) to this file, only after this you can close the file. You also can choose the format and several other options for example the commands below allow save trees with two distinct formats.

tsave *[your tree file name].tre; save .; tsave/; [for save all trees and open in the treeview or figtree]

tsave [your tree file name].ctf; save .; tsave/; [best format to work in tnt]

Are you sure in had read carefully this page below and its associated pages?

http://tnt.insectmuseum.org/index.php/Tree_files

Best wishes,

Ângelo