133 lines
3.3 KiB
Markdown
133 lines
3.3 KiB
Markdown
# TNT Script used by Guoyi
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The TNT script follows MIT license.
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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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- Extended implied weighting with K value setting (default, default K=12) or implied weighting with K value setting (default K=12) or equal weighting.
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- Search trees via implicit enumeration (ntax<=25, but not for eiw) or TBR Mult (1000 times) with branch swapping (25<ntax<75, also for ntax<=25 with eiw) or Mult with branch swapping and Xmult (use random sectorial searches, produce 1,000 hits to best length and stop, 10 cycles of drifting, ratchet and fusing) (ntax>=75).
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- Perform Strict consensus / Majority-rule consensus / Half strict consensus.
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- Calculate jackknifing (1,000 times), bootstrap (1,000 times) and Relative Bremer support.
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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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For Windows users
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```
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tnt run guoyi.run filename datatype weight 0/K cons resample prefix;
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```
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For Linux and Mac users
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```
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tnt run guoyi.run filename datatype weight K cons resample prefix,
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```
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- datatpye should be `32`, `dna`, `prot`, `num`
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- num=number, dna=DNA, prot=protein, 32=max number allowed (default)
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- weight should be `iw`, `ew`, `eiw`
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- iw=implied weight, ew=equal weight, eiw=extended implied weight (default) N.B. ew must followed 0 (the K value position for ew iw and eiw)
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- K is `12` (default) following Goloboff et al. 2017 (Cladistics 34: 407–437)
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- it must more than 0
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- cons should be `str`, `mjr`, `hlf`
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- mjr=majority rule, hlf=half, str=strict (default)
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- resample should be sum of what you want
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- jak=1, boot=2, bremer=4 sym=8 i.e. jak+boot+sym+bremer=15 (default)
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- prefix can be empty or a string
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- default is empty
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## Results
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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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- `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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