bootstrap values shown on the strict consensus tree

[haixing]

Hello, everyone,
I am a paleontologist from China. Recently, I have used TNT for
my phylogenetic analysis. I want to calculate the bootstrap values of
the strict consensus tree using TNT. But I don't know how to calculate
them. When I implement "traditional search" from "analyze" and then
click "consensus" from "Trees", the strict consensus tree will be
shown in full screen. But I cannot obtain the bootstrap values
further. If I use "resampling" option, the tree is not same as the
strict consensus tree and the same one obtained from "Bremer support".
I hope you can help me. Thank you very much for your generous help.
Best Wishes!

Yours,

[sant...@yahoo.com.cn]

[Alberto Rodríguez Rodríguez]

Hi. I believe that this procedure might work:

1- do the analisys and estimates the strict consensus (you have to save this consensus to RAM)

2- As you have saved the strict consensus, you have to deactivate the other trees.

3-When you have only one tree active (strict consensus tree), you do the bootstrap.

Good luck.

 

2011/9/23 sant...@yahoo.com.cn <sant...@yahoo.com.cn>

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[J. Salvador Arias]

Hi

As Alberto says, the first thing is to be sure that you save the tree
when doing the consensus (check “save to RAM” in the consensus tree
dialog)

You will see something like this in the log:
“...
Strict consensus of 56 trees (0 taxa excluded) calculated, as tree 56
0.03 secs.”

Take note of the number of the strict consensus tree.

In the resampling dialog, there is a panel called “Cutoff”, select the
option “Use groups from tree” and select the tree number of the strict
consensus (in this example, the 56).

There is a lot of different things in the resampling dialog, make sure
you select the bootstrap and the support measure that you want (by
default, it uses GC [see Goloboff et al. 2003,
http://dx.doi.org/10.1111/j.1096-0031.2003.tb00376.x] but more
probably you are expecting absolute frequencies).

If you have preview trees active (the default, you can select it with
“Format” menu), then the tree with the support values will be shown in
the screen , press “M” to save the tree as a windows metafile. Another
option is to open an output (in the file menu) as a metafile, do the
resampling, and then close the metafile.

Hope this will help you,
Salvador

2011/9/23 Alberto Rodríguez Rodríguez <arr....@gmail.com>:

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