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# guoyi.run
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[](https://doi.org/10.5281/zenodo.8431529)
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TNT Script for Maximum Parsimony Analysis (Phylogeny)
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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 50 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 (without bremer support variations) / Half strict consensus (without bremer support variations).
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- Calculate relative Bremer support, jackknifing (1,000 times), bootstrap (1,000 times) and symmetric resampling (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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For Windows users
```
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tnt run guoyi.run filename datatype weight 0/K cons resample prefix;
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```
For Linux and Mac users
```
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tnt run guoyi.run filename datatype weight 0/K cons resample prefix,
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```
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- datatype should be `32` , `dna` , `prot` , `num` or any types tnt allowed
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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–
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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)
- resample should be sum of what you want
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- relative bremer support (rbrs)=0.1, bremer support (brs)=0.2, jackknifing (jak)=1, bootstrap (boot)=2, symmetric resampling (sym)=4 i.e. rbrs+jak+boot+sym=7.1 (default)
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- prefix can be empty or a string
- 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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- `*.tre` are trees with taxname, `*_no.tre` are trees without taxname.
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- `*.tnt.tre` can be read by TNT/WinClada directly.
- `*.ctf` can only be read by TNT via `shortread` .
- `*.svg` is the tree file, which can be edited by [inkscape ](https://inkscape.org )
- `original*` is the consensus tree.
- `apo.tre` is the apomorphic character mapping tree.
- `resample.tre` is the consensus tree with support.
- `trees*.tre` contains he MPTs.
- `resample/apo.log` contains the tree tags.
- `eiw.log` contains character concavities.
- `homo.log` contains homoplasy report of all characters.
- `report.log` contains CI RI TL.
- `winclada.ss` includes data matrix and consensus tree and it can be read by winclada directly.
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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. This script follows MIT License.
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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>
```
