133 lines
3.3 KiB
Markdown
133 lines
3.3 KiB
Markdown
# 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: 407–437)
|
||
|
||
- 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, relative 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>
|
||
```
|