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https://github.com/starsareintherose/tnt_script
TNT Script for Maximum Parsimony Analysis
https://github.com/starsareintherose/tnt_script
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TNT Script for Maximum Parsimony Analysis
- Host: GitHub
- URL: https://github.com/starsareintherose/tnt_script
- Owner: starsareintherose
- License: mit
- Created: 2022-03-02T00:49:03.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2024-12-06T04:13:04.000Z (about 2 months ago)
- Last Synced: 2024-12-06T05:19:50.027Z (about 2 months ago)
- Language: C++
- Homepage: https://doi.org/10.5281/zenodo.8431529
- Size: 120 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# guoyi.run
[](https://doi.org/10.5281/zenodo.8431529)
TNT Script for Maximum Parsimony Analysis (Phylogeny)
## 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=75).
- Perform Strict consensus / Majority-rule consensus (without bremer support variations) / Half strict consensus (without bremer support variations).
- Calculate relative Bremer support, jackknifing (1,000 times), bootstrap (1,000 times) and symmetric resampling (1,000 times).
- 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 0/K cons resample prefix,
```
- datatype should be `32`, `dna`, `prot`, `num` or any types tnt allowed
- 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
- 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)
- prefix can be empty or a string
- default is empty
## Results
- Results instructions are at the end of `tnt.log`.
- `*.tre` are trees with taxname, `*_no.tre` are trees without taxname.
- `*.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, which can be read by figtree after processing by tnt2figtree.
- `trees*.tre` contains he MPTs, which can be read by figtree after processing by tnt2figtree.
- `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.
- `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. This script follows MIT License.
# Further information
To make tnt exported trees can be readable by WinClada (Nixon, 2021) and FigTree, please check tnt2winclada and tnt2figtree in this repository.
runwincladtree.run can handle [wincladtree script](https://www.lillo.org.ar/phylogeny/tnt/scripts/wincladtree.run) with input file which must be $(PREFIX).winclada.ss or winclada.tree.