2023-02-26 02:42:56 +08:00
|
|
|
# TNT Script used by Guoyi
|
|
|
|
|
|
2023-02-27 01:35:38 +08:00
|
|
|
This script follows MIT and part of script is from setk.run belonging to Salvador Arias (Instituto Miguel Lillo, San Miguel de Tucumán, Argentina).
|
2023-02-26 02:42:56 +08:00
|
|
|
|
2023-02-26 03:32:18 +08:00
|
|
|
## Usage
|
2023-02-26 02:42:56 +08:00
|
|
|
|
2023-02-27 01:24:22 +08:00
|
|
|
- Place this script and your tnt matrix under the folder that you call `tnt` or `exe` file is placed
|
2023-02-26 03:45:29 +08:00
|
|
|
|
2023-02-27 01:24:22 +08:00
|
|
|
- Enter `tnt`
|
2023-02-26 03:32:18 +08:00
|
|
|
|
2023-02-27 01:24:22 +08:00
|
|
|
- Enter command `guoyi filename;`
|
2023-02-26 03:32:18 +08:00
|
|
|
|
2023-02-27 01:24:22 +08:00
|
|
|
## Functions
|
2023-02-26 03:32:18 +08:00
|
|
|
|
2023-02-27 01:24:22 +08:00
|
|
|
- Estimated implied weighting K value.
|
2023-02-26 03:45:29 +08:00
|
|
|
|
2023-02-27 01:24:22 +08:00
|
|
|
- Search trees via TBR Mult and Xmult.
|
2023-02-26 03:45:29 +08:00
|
|
|
|
2023-02-27 01:24:22 +08:00
|
|
|
- Perform Strict consensus.
|
|
|
|
|
|
|
|
|
|
- Calculate Relative Bremer support, jackknifing, and bootstrap.
|
|
|
|
|
|
|
|
|
|
- Calculate TL, CI, and RI.
|
2023-02-26 03:45:29 +08:00
|
|
|
|
2023-02-26 03:32:18 +08:00
|
|
|
## Options
|
2023-02-26 02:42:56 +08:00
|
|
|
|
2023-02-27 01:24:22 +08:00
|
|
|
- Results instructions are at the end of `tnt.log`.
|
|
|
|
|
|
2023-02-27 01:37:48 +08:00
|
|
|
- `trees.tre`, `con.tre` are trees with taxaname.
|
2023-02-26 02:42:56 +08:00
|
|
|
|
2023-02-27 01:37:48 +08:00
|
|
|
- `trees_no.tre`, `con_no.tre` are trees without taxaname.
|
|
|
|
|
|
|
|
|
|
- `con_no.tre` can be put into Winclada with your tnt matrix file `filename`.
|
2023-02-26 02:42:56 +08:00
|
|
|
|
2023-02-27 01:24:22 +08:00
|
|
|
- `nelsen` can be replaced by `majority`.
|
2023-02-26 02:42:56 +08:00
|
|
|
|
2023-02-27 01:24:22 +08:00
|
|
|
- `xmult` and `mult` replications and hold trees number can be adjusted.
|
2023-02-26 02:42:56 +08:00
|
|
|
|
