Basic Newbie Question

[Stu]

Hi, I'm hoping to try out TNT using the command line Mac 64-bit
version but I'm stalled at the xread command. I've tried loading Nexus
and Hennig format files (exported from PAUP*), and the sample tnt
files that came with the program and I get the same error with all of
them. Example below:


tnt*>xread zilla.tnt ;
Must specify number of
characters
xread zilla.tnt ;

I'd greatly appreciate any help!
Stu

[ross.mounce]

Dear Stu,

The quick answer is you're probably using the wrong command for what
you want to do.

I *think* xread is generally used for creating random (simulated)
matrices:
e.g. xread /10 10 2; http://tnt.insectmuseum.org/index.php/Commands/xread

Assuming you already have data files you want to load into TNT
you probably may want to use 'run' instead http://tnt.insectmuseum.org/index.php/Commands/run
e.g.

run zilla.tnt;
(then use subsequent commands to analyse or explore the dataset)

Regards,

Ross

[Nam Nguyen]

Dear Stu or Ross,

I have a similar problem, in that I cannot seem to load a nexus file
from tnt. I've exported my character matrix and tree using TNT to a
nexus file. If I want to load the matrix and tree for later analysis,
I'm not sure how to do so without converting to a tnt file. I've
tried run test.tre, but I get the following error message:

$tnt*>run test.tree

Reading from test.tre
Running test.tre (with no arguments)
No command!
Error reading line 3 of test.tre
#NEXUS begin data; d
^

I've looked at the wiki, and the wiki mentions that it is possible to
import nexus files, but I cannot find the commands to do so from the
command line. Any help would be much appreciated.

Here's my nexus file:
#NEXUS
begin data;
dimensions ntax=4 nchar=4;
format missing=? symbols="0~1";
matrix
0 1010
1 1010
2 1111
3 0101
;
end;

begin trees ;
tree tnt_1 = [&U]
(0 ,(1 ,(2 ,3 )));

Sincerely,
Nam

On Apr 6, 12:39 pm, "ross.mounce" <ross.mou...@gmail.com> wrote:
> Dear Stu,
>
> The quick answer is you're probably using the wrong command for what
> you want to do.
>
> I *think* xread is generally used for creating random (simulated)
> matrices:
> e.g.  xread /10 10 2;  http://tnt.insectmuseum.org/index.php/Commands/xread
>
> Assuming you already have data files you want to load into TNT

> you probably may want to use 'run' insteadhttp://tnt.insectmuseum.org/index.php/Commands/run

[Santiago Catalano]

Dear Nam,

Just replace the names of the taxa by letters (instead of the numbers).

best wishes,

santiago

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--
Dr. Santiago A. Catalano
Fundación Miguel Lillo - INSUE 

CONICET
SM Tucumán - Tucumán
Argentina

[Nam Nguyen]

Thank you for your reply. I determined the problem was I had macro
language on. Turning it off solved my problem.

Sincerly,
Nam

> >http://groups.google.com/group/tnt-tree-analysis-using-new-technology...
> > .