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# TNT Script used by Guoyi
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The TNT script follows MIT and part of script is from setk.run belonging to Salvador Arias (Instituto Miguel Lillo, San Miguel de Tucumán, Argentina).
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## Usage
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- Place this script and your matrix tnt file `filename` under the folder that you call `tnt` or `exe` file is placed
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- Enter `tnt`
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- Enter command `guoyi filename;`
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## Functions
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- Estimate implied weighting K value.
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- Search trees via TBR Mult (1000 times) and Xmult (use random sectorial searches, produce 1,000 hits to best length and stop, 10 cycles of drifting, ratchet and fusing).
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- Perform Strict consensus.
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- Calculate Relative Bremer support, jackknifing (1,000 times), and bootstrap (1,000 times).
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- Map apomorphic characters on the consensus tree.
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- Calculate TL, CI, and RI.
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## Options
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- Results instructions are at the end of `tnt.log` .
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- `trees.tre` , `resample.tre` are trees with taxname.
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- `trees_no.tre` , `resample_no.tre` are trees without taxname.
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- `nelsen` can be replaced by `majority` .
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- `xmult` and `mult` replications and hold trees number can be adjusted.
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- `winclada.tre` can be transferred to the acceptable format for WinClada by tnt2winclada and the output file can be put into Winclada with your tnt matrix file `filename` for mapping apomorphic characters and homoplasy.
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## Cite
Cite this script is mandatory, list me (Guoyi Zhang) in your Acknowledgements is recommended.
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# TNT2WinClada
```
~|~|\ |~|~ ~) | |o._ |~| _ _ | _
| | \| | /_ \/\/ || ||_|(_|(_|(_|
MIT, Guoyi Zhang, 2023
```
## Function
Convert TNT output tree file without tags and taxname, e.g. `winclada.tre` produced by TNT script, to WinClada acceptable format tree.
## Compile
### Linux & Unix
```
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mkdir -p build & & cd build
cmake ..
make & & make install
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```
### Windows
```
cl /EHsc tnt2winclada.cpp
```
## Usage
```
tnt2winclada -i ${input_file} -o ${output_file}
```
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Interactive commands are also available.
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```
tnt2winclada
~|~|\ |~|~ ~) | |o._ |~| _ _ | _
| | \| | /_ \/\/ || ||_|(_|(_|(_|
TNT2WinClada
MIT, Guoyi Zhang, 2023
please type help to see more commands
tnt2winclada> help
help show interactive commands help
input < filename > input a TNT output tree from the specified file
output < filename > output a winclada accessible tree file
quit quit the program
exit exit the program
tnt2winclada>
```
