468 lines
14 KiB
Plaintext
468 lines
14 KiB
Plaintext
macro=;
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log %7.tnt.log;
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/*Arguments*/
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if ( (argnumber == 0) | (argnumber >7) )
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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 type weight K cons resamp prefix |;
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quote - | - type 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. K of ew must followed 0 (=NA) |;
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quote - | - K is 12 (default) following Goloboff |;
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quote - | et al. 2017 (Cladistics 34: 407–437) |;
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quote - | it must more than 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 - | - resamp should be sum of what you want |;
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quote - | jak=1, boot=2, relative bremer=4 sym=8 |;
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quote - | i.e. jak+boot+sym+bremer=15 (default) |;
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quote - | - prefix can be empty, or a string |;
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quote - | default is empty |;
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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+100;
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taxname=;
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mxram 500;
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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 - | 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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if (%6==8)
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quote - | Symmetric resampling |;
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end
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if (%6==9)
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quote - | Jackknifing and symmetric resampling |;
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end
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if (%6==10)
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quote - | Bootstrap and symmetric resampling |;
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end
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if (%6==11)
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quote - | Jackknifing, bootstrap and symmetric |;
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quote - | resampling |;
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end
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if (%6==12)
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quote - | Symmetric resampling and relative bremer |;
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end
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if (%6==13)
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quote - | Jackknifing, symmetric resampling and |;
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quote - | relative bremer |;
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end
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if (%6==14)
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quote - | Bootstrap, symmetric resampling and |;
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quote - | relative bremer |;
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end
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if (%6==15)
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quote - | Jackknifing, bootstrap, symmetric |;
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quote - | resampling and relative bremer support |;
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end
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end
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if (argnumber<6)
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quote - | Jackknifing, bootstrap, symmetric |;
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quote - | resampling and relative bremer support |;
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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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/*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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/*Search trees*/
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if(argnumber>2)
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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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if (ntax<=74)
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mult=replic 1000 tbr hold 1000;
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bbreak=tbr fill;
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end
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if (ntax>74)
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sect: slack 40;
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xmult=hit 50 replications 20 drift 10 ratchet 10 fuse 10 hold 10 keepall;
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end
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end
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else
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if (ntax<=74)
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mult=replic 1000 tbr hold 1000;
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bbreak=tbr fill;
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else
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sect: slack 40;
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xmult=hit 50 replications 20 drift 20 ratchet 10 fuse 10 hold 10 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 50 replications 20 drift 10 ratchet 10 fuse 10 hold 10 keepall;
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end
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end
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/*Export trees*/
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export= %7.trees.tre;
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taxname-;
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export= %7.trees_no.tre;
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taxname=;
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tsave = %7.trees.ctf;
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tsave *= %7.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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/*Tree vault store*/
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hold /+0;
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tvault >/;
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/*Export consensus tree*/
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tchoose /;
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export - %7.original.tre;
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taxname-;
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export - %7.original_no.tre;
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tsave = %7.original.ctf;
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tsave *= %7.original.tnt.tre;
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/*Caulculate TL/CI/RI score*/
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report-;
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var-;
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var =
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0 themin
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1 themax
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2 CI
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3 RI
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4 TL
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;
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set themin minsteps;
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set themax maxsteps;
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set TL length[0];
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set CI 'themin'/'TL'; /*CI=1 means no homoplasy*/
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set RI ('themax'-'TL')/('themax'-'themin'); /*RI=1 character fits perfetcly*/
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report=;
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/*Apomorphic characters*/
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export = %7.winclada.tre;
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taxname =;
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ttags=;
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apo >0;
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quote - /----------------------------------------------\;
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quote - apomorphy tags start ;
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ttags/;
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quote - apomorphy tags stop ;
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quote - \----------------------------------------------/;
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ttags & %7.apo.svg thickness 7 italics fontsize 15;
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export < %7.apo.tre;
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taxname-;
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export - %7.apo_no.tre;
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ttags-;
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/*Get jak/boot/relative-bremer support*/
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tchoose/;
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ttags=;
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ttags]; /*in one line*/
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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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/* sym=8, */
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/* jak+sym=9, boot+sym=10, bremer+sym=12 */
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/* jak+boot+sym=11, jak+bremer+sym=13, */
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/* boot+bremer+sym=14, */
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/* jak+sym+boot+bremer=15 */
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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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/*symmetric resampling*/
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resample sym 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) | (%6==9) | (%6==11) | (%6==13) | (%6==15))
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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) | (%6==10) | (%6==11) | (%6==14) | (%6==15))
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resample boot replications 1000 from 0;
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end
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if((%6==8) | (%6==9) | (%6==10) | (%6==11) | (%6==12) | (%6==13) | (%6==14) | (%6==15))
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resample sym replications 1000 from 0;
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end
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if((%6==4) | (%6==5) | (%6==6) | (%6==7) | (%6==12) | (%6==13) | (%6==14) | (%6==15))
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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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/*Export consensus tree with supports*/
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ttags & %7.resample.svg thickness 7 italics fontsize 15;
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quote - /----------------------------------------------\;
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quote - resample tags start ;
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ttags/;
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quote - resample tags stop ;
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quote - \----------------------------------------------/;
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export < %7.resample.tre;
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taxname-;
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export - %7.resample_no.tre;
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ttags-;
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/*Report CI/RI/TL */
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macfloat 3;
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quote Consistency Index (CI) is 'CI';
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quote Retention Index (RI) is 'RI';
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quote Tree Length (TL) is 'TL';
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/*Report*/
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quote - /----------------------------------------------\;
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quote - | The analysis has been finished. |;
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quote - | The file `tnt.log` contains |;
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quote - | K, TL, CI and RI |;
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quote - | The file `trees*.tre` contain |;
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quote - | trees found by mult and xmult |;
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quote - | The file `original*.tre` contain |;
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quote - | strict consensus tree without label |;
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quote - | The file `resample*.tre` contain |;
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quote - | consensus tree with support |;
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quote - | The file `apo*.tre` contain |;
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quote - | tree with apomorphic character |;
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quote - | The file `*_no.tre` contain |;
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quote - | tree with `taxname-` |;
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quote - | The file `*.ctf` tree file is |;
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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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if (%6==8)
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quote - | symmetric resampling |;
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end
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if (%6==9)
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quote - | Jackknifing and symmetric resample |;
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end
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if (%6==10)
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quote - | Bootstrap and symmetric resample |;
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end
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if (%6==11)
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quote - | jackknifing, bootstrap and |;
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quote - | symmetric resample |;
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end
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if (%6==12)
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quote - | relative bremer support and |;
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quote - | symmetric resampling |;
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end
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if (%6==13)
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quote - | Jackknifing, symmetric resample and |;
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quote - | relative bremer support |;
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end
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if (%6==14)
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quote - | bootstrap, symmetric resmaple and |;
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quote - | relative bremer support |;
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end
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if (%6==15)
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quote - | jackknifing, bootstrap, symmetric |;
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quote - | resample and relative bremer support|;
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end
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else
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quote - | jackknifing, bootstrap, symmetric |;
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quote - | resample and relative bremer support|;
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end
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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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quote - | converted by tnt2winclada |;
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quote - \----------------------------------------------/;
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/*Quit*/
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zzz;
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