how to perform this command
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min wang
Dec 14, 2011, 4:16:42 AM12/14/11
to TNT-Tree Analysis using New Technology
Hi, I'm a master students interested in the fossil birds from the
paleogene. I have a problem about use TNT in my works. I used the data
matrix of this paper (The deep divergences of neornithine birds: a
phylogenetic analysis of morphological characters, Mayr & Clarke,
2003), and run the TNT with the raw matrix without my specimens, but
the trees I got are quite different from that paper. Even I tried this
in the PAUP, but still largely different .
paleogene. I have a problem about use TNT in my works. I used the data
matrix of this paper (The deep divergences of neornithine birds: a
phylogenetic analysis of morphological characters, Mayr & Clarke,
2003), and run the TNT with the raw matrix without my specimens, but
the trees I got are quite different from that paper. Even I tried this
in the PAUP, but still largely different .
The paper describes the command used in the analysis, and I list them
below:
1. One thousand replicates of random stepwise addition (branch
swapping: tree-bisection-reconnection) were performed holding only one
tree at each step.
2. No more than 10 trees one step longer than the shortest were
retained in each replicate.
3. Branches were collapsed to create soft polytomies if the minimum
branch length was equal to zero.
I still do not understand the second line of command (No more than 10
trees one step longer than the shortest were retained in each
replicate), or how to perform in TNT.
It would mean a lot to me, if you can give me some advice about this.
Thank you for your help.
Marcos Mirande
Dec 14, 2011, 7:02:03 AM12/14/11
to tnt-tree-analysis-u...@googlegroups.com
Hi Min. I'm just reading that paper and it's also not clear for me what they did.
Apparently they did 1000 RAS keeping only one tree per replication and AFTER that they did some sampling of one-step suboptimal trees in order to jump between islands.
Islands are no more a problem due to rather new methods as ratchet, drifting, sectorial searches, and tree fusing. All of them are implemented in TNT under "new technology searches" (or command xmult). However, with the size of that dataset, I think new methods are not necessary at all in this case. If you do 100 RAS keeping 10 trees per replication, and after that you swap trees on memory (to found all or a good sample of optimal trees), you should obtain the correct results. The option of swapping memory trees is into the "traditional searches" menu (or simply with the command bbreak).
Cheers, Marcos.
--
Juan Marcos Mirande
Fundación Miguel Lillo - CONICET
Miguel Lillo 251
(4000) San Miguel de Tucumán
Argentina
Apparently they did 1000 RAS keeping only one tree per replication and AFTER that they did some sampling of one-step suboptimal trees in order to jump between islands.
Islands are no more a problem due to rather new methods as ratchet, drifting, sectorial searches, and tree fusing. All of them are implemented in TNT under "new technology searches" (or command xmult). However, with the size of that dataset, I think new methods are not necessary at all in this case. If you do 100 RAS keeping 10 trees per replication, and after that you swap trees on memory (to found all or a good sample of optimal trees), you should obtain the correct results. The option of swapping memory trees is into the "traditional searches" menu (or simply with the command bbreak).
Cheers, Marcos.
2011/12/14 min wang <wangmi...@gmail.com>
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Juan Marcos Mirande
Fundación Miguel Lillo - CONICET
Miguel Lillo 251
(4000) San Miguel de Tucumán
Argentina
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