99 lines
2.3 KiB
Markdown
99 lines
2.3 KiB
Markdown
# 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
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Cite this script is mandatory, list me (Guoyi Zhang) in your Acknowledgements is recommended.
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# TNT2WinClada
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```
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~|~|\ |~|~ ~) | |o._ |~| _ _| _
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MIT, Guoyi Zhang, 2023
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```
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## Function
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Convert TNT output tree file without tags and taxname, e.g. `winclada.tre` produced by TNT script, to WinClada acceptable format tree.
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## Compile
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### Linux & Unix
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```
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mkdir -p build && cd build
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cmake ..
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make && make install
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```
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### Windows
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```
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cl /EHsc tnt2winclada.cpp
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```
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## Usage
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```
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tnt2winclada -i ${input_file} -o ${output_file}
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```
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Interactive commands are also available.
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```
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tnt2winclada
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~|~|\ |~|~ ~) | |o._ |~| _ _| _
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TNT2WinClada
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MIT, Guoyi Zhang, 2023
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please type help to see more commands
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tnt2winclada> help
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help show interactive commands help
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input <filename> input a TNT output tree from the specified file
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output <filename> output a winclada accessible tree file
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quit quit the program
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exit exit the program
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tnt2winclada>
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```
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