2023-10-11 21:59:45 +08:00
# guoyi.run
2023-10-11 22:34:53 +08:00
[](https://doi.org/10.5281/zenodo.8431529)
2023-02-26 02:42:56 +08:00
2023-10-11 22:03:06 +08:00
TNT Script for Maximum Parsimony Analysis (Phylogeny)
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 01:42:50 +08:00
- Place this script and your matrix tnt file `filename` 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
2023-09-14 00:16:32 +08:00
- Extended implied weighting with K value setting (default, default K=12) or implied weighting with K value setting (default K=12) or equal weighting.
2023-02-26 03:45:29 +08:00
2023-10-10 22:57:20 +08:00
- 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).
2023-02-26 03:45:29 +08:00
2023-10-10 22:57:20 +08:00
- Perform Strict consensus / Majority-rule consensus (without bremer support variations) / Half strict consensus (without bremer support variations).
2023-02-27 01:24:22 +08:00
2023-10-10 22:57:20 +08:00
- Calculate relative Bremer support, jackknifing (1,000 times), bootstrap (1,000 times) and symmetric resampling (1,000 times).
2023-02-27 01:24:22 +08:00
2023-02-28 03:26:37 +08:00
- Map apomorphic characters on the consensus tree.
2023-02-27 01:24:22 +08:00
- 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
2023-09-13 21:05:52 +08:00
For Windows users
```
2023-09-14 00:08:43 +08:00
tnt run guoyi.run filename datatype weight 0/K cons resample prefix;
2023-09-13 21:05:52 +08:00
```
For Linux and Mac users
```
2023-10-11 21:59:45 +08:00
tnt run guoyi.run filename datatype weight 0/K cons resample prefix,
2023-09-13 21:05:52 +08:00
```
2023-10-10 22:57:20 +08:00
- datatype should be `32` , `dna` , `prot` , `num` or any types tnt allowed
2023-09-13 21:05:52 +08:00
- num=number, dna=DNA, prot=protein, 32=max number allowed (default)
2023-09-14 00:10:08 +08:00
- weight should be `iw` , `ew` , `eiw`
2023-09-13 21:05:52 +08:00
- 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)
2023-09-14 00:10:08 +08:00
- K is `12` (default) following Goloboff et al. 2017 (Cladistics 34: 407–
2023-09-14 00:08:43 +08:00
- it must more than 0
2023-09-14 00:10:08 +08:00
- cons should be `str` , `mjr` , `hlf`
2023-09-13 21:05:52 +08:00
- mjr=majority rule, hlf=half, str=strict (default)
- resample should be sum of what you want
2023-10-10 22:57:20 +08:00
- 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)
2023-09-13 21:05:52 +08:00
2023-09-14 00:08:43 +08:00
- prefix can be empty or a string
- default is empty
2023-09-13 21:05:52 +08:00
## Results
2023-02-27 01:24:22 +08:00
- Results instructions are at the end of `tnt.log` .
2023-10-10 22:57:20 +08:00
- `*.tre` are trees with taxname, `*_no.tre` are trees without taxname.
2023-02-27 01:37:48 +08:00
2023-10-10 22:57:20 +08:00
- `*.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.
2024-01-14 22:30:04 +08:00
- `resample.tre` is the consensus tree with support, which can be read by figtree after processing by tnt2figtree.
2023-10-10 22:57:20 +08:00
2024-01-14 22:30:04 +08:00
- `trees*.tre` contains he MPTs, which can be read by figtree after processing by tnt2figtree.
2023-10-10 22:57:20 +08:00
- `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.
2023-02-26 02:42:56 +08:00
2023-02-28 03:26:37 +08:00
- `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.
2023-07-17 06:31:26 +08:00
## Cite
2023-10-11 22:03:06 +08:00
Cite this script is mandatory, list me (Guoyi Zhang) in your Acknowledgements is recommended. This script follows MIT License.
2023-07-17 06:31:26 +08:00
2024-01-14 22:30:04 +08:00
# Further information
2023-02-28 03:26:37 +08:00
2024-01-14 22:30:04 +08:00
To make tnt exported trees can be readable by WinClada (Nixon, 2021) and FigTree, please check tnt2winclada and tnt2figtree in this repository.
