108 lines
3.8 KiB
Markdown
108 lines
3.8 KiB
Markdown
# guoyi.run
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[](https://doi.org/10.5281/zenodo.8431529)
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TNT Script for Maximum Parsimony Analysis (Phylogeny)
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## Usage
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- Place this script and your matrix tnt file `filename` under the folder that you call `tnt` or `exe` file is placed
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- Enter `tnt`
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- Enter command `guoyi filename;`
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## Functions
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- Extended implied weighting with K value setting (default, default K=12) or implied weighting with K value setting (default K=12) or equal weighting.
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- 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).
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- Perform Strict consensus / Majority-rule consensus (without bremer support variations) / Half strict consensus (without bremer support variations).
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- Calculate relative Bremer support, jackknifing (1,000 times), bootstrap (1,000 times) and symmetric resampling (1,000 times).
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- Map apomorphic characters on the consensus tree.
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- Calculate TL, CI, and RI.
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## Options
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For Windows users
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```
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tnt run guoyi.run filename datatype weight 0/K cons resample prefix;
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```
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For Linux and Mac users
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```
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tnt run guoyi.run filename datatype weight 0/K cons resample prefix,
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```
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- datatype should be `32`, `dna`, `prot`, `num` or any types tnt allowed
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- num=number, dna=DNA, prot=protein, 32=max number allowed (default)
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- weight should be `iw`, `ew`, `eiw`
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- 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)
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- K is `12` (default) following Goloboff et al. 2017 (Cladistics 34: 407–437)
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- it must more than 0
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- cons should be `str`, `mjr`, `hlf`
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- mjr=majority rule, hlf=half, str=strict (default)
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- resample should be sum of what you want
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- 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)
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- prefix can be empty or a string
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- default is empty
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## Results
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- Results instructions are at the end of `tnt.log`.
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- `*.tre` are trees with taxname, `*_no.tre` are trees without taxname.
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- `*.tnt.tre` can be read by TNT/WinClada directly.
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- `*.ctf` can only be read by TNT via `shortread`.
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- `*.svg` is the tree file, which can be edited by [inkscape](https://inkscape.org)
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- `original*` is the consensus tree.
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- `apo.tre` is the apomorphic character mapping tree.
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- `resample.tre` is the consensus tree with support, which can be read by figtree after processing by tnt2figtree.
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- `trees*.tre` contains he MPTs, which can be read by figtree after processing by tnt2figtree.
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- `resample/apo.log` contains the tree tags.
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- `eiw.log` contains character concavities.
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- `homo.log` contains homoplasy report of all characters.
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- `report.log` contains CI RI TL.
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- `winclada.ss` includes data matrix and consensus tree and it can be read by winclada directly.
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- `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.
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## Cite
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Cite this script is mandatory, list me (Guoyi Zhang) in your Acknowledgements is recommended. This script follows MIT License.
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# Further information
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To make tnt exported trees can be readable by WinClada (Nixon, 2021) and FigTree, please check tnt2winclada and tnt2figtree in this repository.
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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.
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