tree buffer full

[viviana]

Hi All,

I am performing a run with 35 taxa and 25 character, and the following
command:

piwe [ 0.25 0.15 0.10 ;
mult= tbr replic 100 hold 6000;
resample boot replications 1000;
taxname;
tsave trees.tre;
nelsen 6000
tsave cons.tre;

but after replication 7, the search stops because of "tree buffer
full".

Is there someone that can help me?

Thanks a lot
Viviana

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[Marcos Mirande]

Hi again Viviana

By default TNT have space to keep up to 100 trees. If you run 100 replicates holding up to 6000 trees by rep (what a strange strategy, by the way) you'll need space for 600000 trees in memory. You can get that by typing "hold 600000" in the command-line.

Surely would be better to hold less trees by repl (10 or so) and increase the number of replicates, and swap trees of memory (i. e. hold 10000; mult= tbr repl 1000 hold 10; bb;) 

Or even better, you may use the "new technologies searches", which surely will produce the same results (the optimal ones) in much less time.

Cheers, Marcos.

--
Juan Marcos Mirande
Fundación Miguel Lillo - CONICET
Miguel Lillo 251
(4000) San Miguel de Tucumán
Argentina

[J. Salvador Arias]

Hi Viviana

Apart from Marcos comments, there are some small problems with your
command sequence.

First I guess you want to save all trees from the original search.
With tsave, you only open the tree file, but not save any tree. You
must use save (tree range) to save the trees, and the close the tree
file...

something like this

tsave trees.tre ; save ; tsave / ;

the “tsave/;” close the tree file.

if you want to save an specific tree, you can set a tree scope, just
as marcos explain in a previous post about apo (I.e. save 0 3, will
save trees 0 and 3. whereas save 0.3 will save trees from 0 to 3,
without any scope, as in the example, it save all trees in memory).

Nest you make nelsen for a strinct consensus, but with nelsen 6000,
you will produce the strict consensus of tree 6000 (that is, not
consensus at all!). Just type “nelsen ;” to show the strict consesus
of all trees. Just as in save and other commands, scopes are possible.

Then, you try to save the consensus. But nelsen just show the tree, to
keep the tree, type “nelsen* ;” the tree is save as the last tree in
memory (the program report the number of the tree). So to save the
consensus, this line will do it (where X is the number of the
consensus):

tsave cons.tre ; save X ; tsave / ;

There a helpful trick (if you are using a batch sequence of commands,
or a macro) to save the consensus without knowing its number, it is
using strict within keys:

tsave cons.tre ; save {strict} ; tsave /;

Note that by default tsave save trees in binary format, you will only
able to open them with TNT. Maybe you want to open in another program
for tree printing. Then you must use the typical parenthical notation.
You can do it typing “tsave*” when open the tree file, for example

tsave* toprint.tre ; save {strict} ; tsave /;

Hope this will help you
Salvador


J. Salvador Arias
Becario CONICET
INSUE, Instituto Miguel Lillo, Miguel Lillo 205
4000 San Miguel de Tucumán, Argentina

[viviana]

Hi Salvador and Marcos,

thank you very much for your very important advices!!!!
All in all, I am realising I switched "hold" and "rep" numbers!

Thanks!
Viviana

> Para tener acceso a más opciones, visita el grupo enhttp://groups.google.com/group/tnt-tree-analysis-using-new-technology....

[viviana]

Hi again,

I modified my setting as follows:

piwe [ 0.25 0.15 0.10 ;
mult= tbr replic 100 hold 10;
resample=boot replications 1000;
Bsupport*[;
taxname;
tsave treesVitr.tre; save;tsave/;
nelsen*;
tsave* toprintconsVitr.tre; save {strict};tsave/;

then, I am not able to save also the branch supports on the tree file.
I was able to visualise apomorphs on the TNT display but I cannot
save them. How can I do that?

Thanks a lot!
Viviana

[Marcos Mirande]

Hi Viviana

The .tre file only saves the tree(s), not the support indices. If you wanna save the supports you have to calculate them and save the tree as .emf from the graphic mode (when "preview mode" is on). You can save the tree from TNT graphic mode by clicking "M" when such tree is in the screen. 

Also you could uncheck "preview trees", left the tree with branch supports be printed in the TNT text-buffer, and save it as text. This is possible with command "log". You only should replace

Bsupport*[;

with

log bremer.txt; Bsupport*[; log/;

Cheers, Marcos.

2010/4/20 viviana <fiorentin...@googlemail.com>

--
Juan Marcos Mirande
Fundación Miguel Lillo - CONICET
Miguel Lillo 251
(4000) San Miguel de Tucumán

Argentina

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[J. Salvador Arias]

Hi Viviana

You can also save support values on command mode using the command
ttag, I not remember exactly how it works (I always have to do some
tries before “re-learn” again :P). I guess that something like this
will work:

ttags =;

This command enables the use of tags

Then to save the tags you can use ttags/;

log supvals.txt ;
ttags / ;
log /;

This file will save the ttags in supvals.txt, so in the next run of
TNT you can load the tags using pr supvals.txt ; after reading the
trees.

This command is also available under windows with the menus... (here I
don't have a win version, so I don't remember the menu sequence), or
using the command line.

Check this howto in the wiki:
http://tnt.insectmuseum.org/index.php/How_to_print_resampling_values_and_bremer_values_on_a_consensus_tree

and also the help about ttags:
http://tnt.insectmuseum.org/index.php/Commands/ttags

Hope this will help you
Salvador


J. Salvador Arias
Becario CONICET
INSUE, Instituto Miguel Lillo, Miguel Lillo 205
4000 San Miguel de Tucumán, Argentina

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[viviana]

Hi,

thank you both very much!

now, I am able to save the branch supports in the TNT text-buffer and
save it as text.

But I cannot still save apomorphies related to a specific tree. Is it
possible to do that?

Thanks so much again!

V.

[jozeca...@gmail.com]

Hello everyone,

my name is José Ricardo and I would like to know why TNT gives me the following message "No space to store new trees" even I  set TNT for holding up to 10000000 when conducting a loop with 500 replicates? I use keep 0 to clear the tree buffer. 

My searches are mult 1000 = hold 10 tbr; bb=tbr inside such loop.

Someone has any idea?