105 lines
3.7 KiB
Markdown
105 lines
3.7 KiB
Markdown
# 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<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).
|
||
|
||
- 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.
|