polish: update parameters

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kuoi 2023-09-13 21:05:52 +08:00
parent ce2cc5a662
commit 12829a96af

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@ -12,11 +12,11 @@ The TNT script follows MIT and part of script is from setk.run belonging to Salv
## Functions
- Estimate implied weighting K value.
- Extended implied weighting with K value setting (default, default K=12) or implighted weighting with K value setting (default K=12) or equal weighting.
- Search trees via TBR Mult (1000 times) and Xmult (use random sectorial searches, produce 1,000 hits to best length and stop, 10 cycles of drifting, ratchet and fusing).
- Search trees via implicit enumeration (ntax<=25) or TBR Mult (1000 times) (25<ntax<75) or Mult and Xmult (use random sectorial searches, produce 1,000 hits to best length and stop, 10 cycles of drifting, ratchet and fusing) (ntax>=75).
- Perform Strict consensus.
- Perform Strict consensus / Majority-rule consensus / Half strict consensus.
- Calculate Relative Bremer support, jackknifing (1,000 times), and bootstrap (1,000 times).
@ -26,16 +26,42 @@ The TNT script follows MIT and part of script is from setk.run belonging to Salv
## Options
For Windows users
```
tnt run guoyi.run filename datatype weight 0/K cons resample;
```
For Linux and Mac users
```
tnt run guoyi.run filename datatype weight 0/K cons resample,
```
- datatpye should be `32`, `dna`, `prot`, `num`
- 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)
- cons should be str, mjr, hlf
- mjr=majority rule, hlf=half, str=strict (default)
- resample should be sum of what you want
- jak=1, boot=2, relative bremer=4 i.e. jak+boot+bremer=7 (default)
## Results
- Results instructions are at the end of `tnt.log`.
- `trees.tre`, `resample.tre` are trees with taxname.
- `trees_no.tre`, `resample_no.tre` are trees without taxname.
- `nelsen` can be replaced by `majority`.
- `xmult` and `mult` replications and hold trees number can be adjusted.
- `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