polish: update parameters
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README.md
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README.md
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@ -12,11 +12,11 @@ The TNT script follows MIT and part of script is from setk.run belonging to Salv
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## Functions
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- Estimate implied weighting K value.
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- Extended implied weighting with K value setting (default, default K=12) or implighted weighting with K value setting (default K=12) or equal weighting.
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- 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).
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- 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).
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- Perform Strict consensus.
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- Perform Strict consensus / Majority-rule consensus / Half strict consensus.
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- Calculate Relative Bremer support, jackknifing (1,000 times), and bootstrap (1,000 times).
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@ -26,16 +26,42 @@ The TNT script follows MIT and part of script is from setk.run belonging to Salv
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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;
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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,
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```
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- datatpye should be `32`, `dna`, `prot`, `num`
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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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- 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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- jak=1, boot=2, relative bremer=4 i.e. jak+boot+bremer=7 (default)
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## Results
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- Results instructions are at the end of `tnt.log`.
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- `trees.tre`, `resample.tre` are trees with taxname.
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- `trees_no.tre`, `resample_no.tre` are trees without taxname.
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- `nelsen` can be replaced by `majority`.
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- `xmult` and `mult` replications and hold trees number can be adjusted.
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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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