# TNT Script used by Guoyi

This script follows MIT and part of script is from setk.run belonging to Salvador Arias (Instituto Miguel Lillo, San Miguel de Tucumán, Argentina).

## Usage

- Place this script and your tnt matrix under the folder that you call `tnt` or `exe` file is placed 

- Enter `tnt`

- Enter command `guoyi filename;`

## Functions

- Estimated implied weighting K value.      

- Search trees via TBR Mult and Xmult.     

- Perform Strict consensus.            

- Calculate Relative Bremer support, jackknifing, and bootstrap.

- Calculate TL, CI, and RI. 

## Options

- Results instructions are at the end of `tnt.log`.

- `con.tre`, `con.tre` are trees with taxaname.

- `trees_no.tre`, `bt_no.tre` are trees without taxaname which can be put into Winclada with the `file.tnt`.

- `nelsen` can be replaced by `majority`.

- `xmult` and `mult` replications and hold trees number can be adjusted.