TNT_Script/README.md

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# TNT Script used by Guoyi
The TNT script follows MIT license.
## Usage
- Place this script and your matrix tnt file `filename` under the folder that you call `tnt` or `exe` file is placed
- Enter `tnt`
- Enter command `guoyi filename;`
## Functions
- Extended implied weighting with K value setting (default, default K=12) or implied weighting with K value setting (default K=12) or equal weighting.
- 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).
- Perform Strict consensus / Majority-rule consensus / Half strict consensus.
- Calculate jackknifing (1,000 times), bootstrap (1,000 times) and Relative Bremer support.
- Map apomorphic characters on the consensus tree.
- Calculate TL, CI, and RI.
## Options
For Windows users
```
tnt run guoyi.run filename datatype weight 0/K cons resample prefix;
```
For Linux and Mac users
```
tnt run guoyi.run filename datatype weight K cons resample prefix,
```
- datatpye should be `32`, `dna`, `prot`, `num`
- num=number, dna=DNA, prot=protein, 32=max number allowed (default)
- weight should be `iw`, `ew`, `eiw`
- 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)
- K is `12` (default) following Goloboff et al. 2017 (Cladistics 34: 407437)
- it must more than 0
- cons should be `str`, `mjr`, `hlf`
- mjr=majority rule, hlf=half, str=strict (default)
- resample should be sum of what you want
- jak=1, boot=2, bremer=4 sym=8 i.e. jak+boot+sym+bremer=15 (default)
- prefix can be empty or a string
- default is empty
## Results
- Results instructions are at the end of `tnt.log`.
- `trees.tre`, `resample.tre` are trees with taxname.
- `trees_no.tre`, `resample_no.tre` are trees without taxname.
- `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.
## Cite
Cite this script is mandatory, list me (Guoyi Zhang) in your Acknowledgements is recommended.
# 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
```
mkdir -p build && cd build
cmake ..
make && make install
```
### Windows
```
cl /EHsc tnt2winclada.cpp
```
## Usage
```
tnt2winclada -i ${input_file} -o ${output_file}
```
Interactive commands are also available.
```
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>
```