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5a7faee66e
2 changed files with 40 additions and 283 deletions
40
README.md
40
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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- 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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- Estimate implied weighting K value.
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- Search trees via implicit enumeration (ntax<=25, but not for eiw) or TBR Mult (1000 times) (25<ntax<75, also for ntax<=25 with eiw) 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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- 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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- Perform Strict consensus / Majority-rule consensus / Half strict consensus.
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- Perform Strict consensus.
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- Calculate Relative Bremer support, jackknifing (1,000 times), and bootstrap (1,000 times).
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@ -26,42 +26,16 @@ 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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283
guoyi.run
283
guoyi.run
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@ -1,184 +1,47 @@
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log tnt.log;
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macro=;
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macro=; taxname+1000; taxname=; mxram 10240; nstates 32; nstates NOGAPS;
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/*Arguments*/
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if ( (argnumber == 0) | (argnumber >=7) )
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if ( argnumber != 1 )
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silent -console;
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quote - /----------------------------------------------------\;
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quote - | GUOYI TNT SCRIPT 2022-2023 MIT |;
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quote - | You need to give your filename |;
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quote - | shell> tnt run guoyi.tnt filename, (Linux & Mac) |;
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quote - | shell> tnt run guoyi.run filename(semicolon) (Win) |;
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quote - | ============================== |;
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quote - | === Parameters Details === |;
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quote - | ============================== |;
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quote - | filename datatype weight 0/K cons resample |;
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quote - | - datatpye should be 32, dna, prot, num |;
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quote - | num=number, dna=DNA, prot=protein |;
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quote - | 32=max number allowed (default) |;
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quote - | - weight should be iw, ew, eiw |;
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quote - | iw=implied weight, ew=equal weight |;
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quote - | eiw=extended implied weight (default) |;
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quote - | N.B. ew must followed 0 |;
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quote - | - cons should be str, mjr, hlf |;
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quote - | mjr=majority rule, hlf=half |;
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quote - | str=strict (default) |;
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quote - | - resample should be sum of what you want |;
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quote - | jak=1, boot=2, relative bremer=4 |;
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quote - | i.e. jak+boot+bremer=7 (default) |;
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quote - \----------------------------------------------------/;
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quote - /--------------------------------------------------\;
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quote - | GUOYI TNT SCRIPT 2022-2023 MIT |;
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quote - | You need to give your filename |;
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quote - | shell> tnt run guoyi.tnt filename, (Linux & Mac) |;
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quote - | shell> tnt run guoyi.run filename; (Windows) |;
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quote - \--------------------------------------------------/;
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proc/;
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end
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/*Basic settings*/
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taxname+1000;
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taxname=;
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mxram 10240;
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if(argnumber>=2)
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nstates %2;
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else
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nstates 32;
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end
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nstates NOGAPS;
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/*Set K*/
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if(argnumber>2 )
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if (eqstring [ %3 ew ])
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quote Equal weighting is used;
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if (argnumber>=4)
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if (%4!=0)
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quote Warning: equal weighting %4 should be fullfilled with 0;
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end
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end
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end
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if ((eqstring [ %3 iw ]) | (eqstring [ %3 eiw ]))
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if (argnumber>=4)
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piwe=%4;
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else
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piwe=12;
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end
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end
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else
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piwe=12;
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end
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/*Reopen tnt*/
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procedure %1;
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hold 10000;
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/*Report what will be done*/
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quote - /-----------------------------------------------\;
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if(argnumber>2)
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if (eqstring [ %3 iw ])
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if (argnumber>3)
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quote - | Implied weighting will be used, K is %4. |;
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else
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quote - | Implied weighting will be used, K is 12. |;
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end
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end
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if (eqstring [ %3 eiw ])
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if (argnumber>3)
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quote - | Ex-implied weighting will be used, K is %4. |;
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else
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quote - | Ex-implied weighting will be used, K is 12. |;
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end
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end
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if (eqstring [ %3 ew ])
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quote - | Equal weighting will be used. |;
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end
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else
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quote - | Ex-implied weighting will be used, K is 12. |;
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end
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if (ntax<=25)
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quote - | Implicit enumeration will be performed. |;
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end
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if ((ntax>25) && (ntax < 75))
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quote - | TBR Mult will be performed. |;
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end
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if (ntax>=75)
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quote - | Implied weighting will be estimated. |;
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quote - | TBR Mult and Xmult will be performed. |;
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end
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if (argnumber>=5)
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if (eqstring [ %5 mjr ])
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quote - | Majority-rule consensus will be used. |;
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end
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if (eqstring [ %5 hlf ])
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quote - | Half strict consensus will be used. |;
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end
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if(eqstring [ %5 str ])
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quote - | Strict consensus will be used. |;
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end
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end
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if (argnumber<5)
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quote - | Strict consensus will be used. |;
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end
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if (argnumber>=6)
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if (%6==1)
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quote - | Jackknifing |;
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end
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if (%6==2)
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quote - | Bootstrap |;
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end
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if (%6==3)
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quote - | Jackknifing and bootstrap |;
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end
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if (%6==4)
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quote - | Relative bremer support |;
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end
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if (%6==5)
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quote - | Jackknifing and relative bremer support |;
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end
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if (%6==6)
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quote - | Bootstrap and relative bremer support |;
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end
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if (%6==7)
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quote - | Jackknifing, bootstrap and relative bremer |;
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end
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end
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if (argnumber<6)
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quote - | Jackknifing, bootstrap and relative bremer |;
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end
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quote - | will be shown on the resample.svg. |;
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quote - | Apomorphic characters mapping will be shown |;
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quote - | on the apo.svg and saved to apo*.tre. |;
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quote - | TL, CI and RI will be calculated finally. |;
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quote - \------------------------------------------------/;
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/*Set K*/
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piwe=12;
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/*Reopen tnt*/
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procedure %1;
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hold 10000;
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/*Implied weighting settings*/
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if(argnumber>2)
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if (eqstring [ %3 iw ])
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piwe&;
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end
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if (eqstring [ %3 eiw ])
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xpiwe(*;
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piwe&;
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end
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else
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xpiwe(*;
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piwe&;
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end
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xpiwe(*;
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piwe&;
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/*Search trees*/
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if(eqstring [ %3 ew ] | eqstring [ %3 iw ] )
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if (ntax<=25)
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ienum;
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else
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mult=replic 1000 tbr hold 1000;
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bbreak=tbr fill;
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if (ntax>74)
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sect: slack 1000;
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xmult=hit 1000 noupdate replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
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end
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end
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else
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mult=replic 1000 tbr hold 1000;
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bbreak=tbr fill;
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if (ntax>74)
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sect: slack 1000;
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xmult=hit 1000 noupdate replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
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end
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end
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mult=replic 1000 tbr hold 1000;
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bbreak=tbr fill;
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sect: slack 1000;
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xmult=hit 1000 noupdate replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
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/*Export trees*/
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export= trees.tre;
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@ -189,19 +52,7 @@ tsave = trees.ctf;
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tsave *= trees.tnt.tre;
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/*Consensus tree*/
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if (argnumber<=4)
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nelsen *;
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else
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if (eqstring [ %5 str ])
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nelsen *;
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end
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if (eqstring [ %5 mjr ])
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majority *;
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end
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if (eqstring [ %5 hlf ])
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comcomp *;
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end
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end
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nelsen *;
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/*Tree vault store*/
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hold /+0;
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@ -252,40 +103,15 @@ ttags-;
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tchoose/;
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ttags=;
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ttags]; /*in one line*/
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resample jak replications 1000 from 0;
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/* jak=1, boot=2, bremer=4, */
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/* jak+boot=3, */
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/* jak+brember=5, boot+bremer=6, */
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/* jak+boot+bremer=7, */
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resample boot replications 1000 from 0;
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if (argnumber<=5)
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/*jakknifing*/
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resample jak replications 1000 from 0;
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/*bootstrap*/
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resample boot replications 1000 from 0;
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/*relative bremer*/
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sub 1; hold +1000; bbreak=fill;
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sub 3; hold +3000; bbreak=fill;
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sub 5; hold +5000; bbreak=fill;
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sub 7; hold +7000; bbreak=fill;
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bsupport[;
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else
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if((%6==1) | (%6==3) | (%6==5) | (%6==7))
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resample jak replications 1000 from 0;
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end
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if((%6==2) | (%6==3) | (%6==6) | (%6==7))
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resample boot replications 1000 from 0;
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end
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if((%6==4) | (%6==5) | (%6==6) | (%6==7))
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sub 1; hold +1000; bbreak=fill;
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sub 3; hold +3000; bbreak=fill;
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sub 5; hold +5000; bbreak=fill;
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sub 7; hold +7000; bbreak=fill;
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bsupport[;
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end
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end
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sub 1; hold +1000; bbreak=fill;
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sub 3; hold +3000; bbreak=fill;
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sub 5; hold +5000; bbreak=fill;
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sub 7; hold +7000; bbreak=fill;
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bsupport[;
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/*Export consensus tree with supports*/
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ttags & resample.svg thickness 7 italics fontsize 15;
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@ -325,52 +151,9 @@ quote - | only readable for TNT |;
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quote - | The file `*.tnt.tre` contain |;
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quote - | is the ctf file with taxname |;
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quote - | The file `resample.svg` contain |;
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if (argnumber>=5)
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if(eqstring [ %5 mjr ])
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quote - | majority rule consensus tree with |;
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end
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if(eqstring [ %5 hlf ])
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quote - | half strict consensus tree with |;
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end
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if(eqstring [ %5 str ])
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quote - | strict consensus tree with |;
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end
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else
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quote - | strict consensus tree with |;
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end
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if (argnumber>=6)
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if (%6==1)
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quote - | jackknifing |;
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end
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if (%6==2)
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quote - | bootstrap |;
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end
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if (%6==3)
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quote - | jackknifing and bootstrap |;
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end
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if (%6==4)
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quote - | relative bremer support |;
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end
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if (%6==5)
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quote - | jackknifing and relative bremer |;
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quote - | support |;
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end
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if (%6==6)
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quote - | bootstrap and relative bremer |;
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quote - | support |;
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end
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if (%6==7)
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quote - | jackknifing, bootstrap and |;
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quote - | relative bremer support |;
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end
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else
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quote - | jackknifing, bootstrap and |;
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quote - | relative bremer support |;
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end
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quote - | relative jak, boot and bremer |;
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quote - | support on the tree |;
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quote - | The file `apo.svg` contain the |;
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quote - | tree with apomorphy mapping |;
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quote - | The file `winclada.tre` can be |;
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