malacology/TNT_Script
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polish: update README

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kuoi 2023-10-10 22:57:20 +08:00
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36
README.md
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@ -14,11 +14,11 @@ The TNT script follows MIT license.
- 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 1,000 hits to best length and stop, 10 cycles of drifting, ratchet and fusing) (ntax>=75).
- 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 / Half strict consensus.
- Perform Strict consensus / Majority-rule consensus (without bremer support variations) / Half strict consensus (without bremer support variations).
- Calculate jackknifing (1,000 times), bootstrap (1,000 times) and Relative Bremer support.
- 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.
@ -38,7 +38,7 @@ For Linux and Mac users
tnt run guoyi.run filename datatype weight K cons resample prefix,
```
- datatpye should be `32`, `dna`, `prot`, `num`
- datatype should be `32`, `dna`, `prot`, `num` or any types tnt allowed
- num=number, dna=DNA, prot=protein, 32=max number allowed (default)
@ -56,7 +56,7 @@ tnt run guoyi.run filename datatype weight K cons resample prefix,
- resample should be sum of what you want
- jak=1, boot=2, bremer=4 sym=8 i.e. jak+boot+sym+bremer=15 (default)
- 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
@ -66,9 +66,31 @@ tnt run guoyi.run filename datatype weight K cons resample prefix,
- Results instructions are at the end of `tnt.log`.
- `trees.tre`, `resample.tre` are trees with taxname.
- `*.tre` are trees with taxname, `*_no.tre` are trees without taxname.
- `trees_no.tre`, `resample_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.
- `trees*.tre` contains he MPTs.
- `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.

12
guoyi.run
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@ -506,7 +506,7 @@ quote
/----------------------------------------------\
| The analysis has been finished. |
| The file `tnt.log` contains |
| K, TL, CI and RI |
| the performing details |
| The file `trees*.tre` contain |
| trees found by mult and xmult |
| The file `original*.tre` contain |
@ -520,7 +520,7 @@ quote
| The file `*.ctf` tree file is |
| only readable for TNT |
| The file `*.tnt.tre` contain |
| is the ctf file with taxname |
| is the tre file without taxname |
| The file `resample.svg` contain |;
if ('dostr')
@ -577,14 +577,14 @@ quote
| tree with apomorphy mapping |
| The file `report.log` contains the |
| CI RI TL publish-needed info |
| The file `resample/apo.log` contain the |
| tree tags in text |
| The file `homo.log` contain the report |
| The file `resample/apo.log` contains |
| the tree tags text |
| The file `homo.log` contains the report |
| of character homoplasy |;
if ('doeiw')
quote
| The file `eiw.log` contain the report |
| The file `eiw.log` contains the report |
| of character concavities |;
end