add: relative bremer support; polish: bremer related search
This commit is contained in:
parent
cd60624662
commit
b2c852eabe
1 changed files with 548 additions and 313 deletions
861
guoyi.run
861
guoyi.run
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@ -5,41 +5,43 @@ 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, 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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quote
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/----------------------------------------------------\
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| GUOYI TNT SCRIPT 2022-2023 MIT |
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| You need to give your filename |
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| shell> tnt run guoyi.tnt filename, (Linux & Mac) |
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| shell> tnt run guoyi.run filename(semicolon) (Win) |
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| ============================== |
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| === Parameters Details === |
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| ============================== |
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| filename type weight K cons resamp prefix |
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| - type should be 32, dna, prot, num |
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| num=number, dna=DNA, prot=protein |
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| 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 |
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| eiw=extended implied weight (default) |
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| N.B. K of ew must followed 0 (=NA) |
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| - K is 12 (default) following Goloboff |
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| et al. 2017 (Cladistics 34: 407–437) |
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| it must more than 0 |
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| - cons should be str, mjr, hlf |
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| mjr=majority rule, hlf=half |
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| str=strict (default) |
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| - resamp should be sum of what you want |
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| jak=1, boot=2, sym=4 relative-bremer |
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| (rbr)=0.1, bremer(br)=0.2 |
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| i.e rbr+br+jak+boot+sym=7.3 (default) |
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| - prefix can be empty, or a string |
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| default is empty |
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\----------------------------------------------------/;
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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 500;
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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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@ -51,19 +53,19 @@ nstates NOGAPS;
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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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if ((argnumber>=4) && (%4 != 0))
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errmsg equal weighting %4 should be fullfilled with 0;
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end
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end
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else
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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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errmsg %3 must be ew iw or eiw;
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end end
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else
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piwe=12;
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end
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@ -73,124 +75,211 @@ 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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quote
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/-----------------------------------------------\;
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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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quote
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| 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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quote
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| Implied weighting will be used, K is 12. |;
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end
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end
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else
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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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quote
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| 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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quote
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| Ex-implied weighting will be used, K is 12. |;
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end
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end
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else
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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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quote
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| Equal weighting will be used. |;
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else
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errmsg %3 must be ew iw or eiw;
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end end end
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else
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quote - | Ex-implied weighting will be used, K is 12. |;
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quote
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| 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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quote
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| Implicit enumeration will be performed. |;
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else
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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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quote
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| TBR Mult will be performed. |;
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else
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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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quote
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| Xmult will be performed. |;
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end end end
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if (argnumber<=5)
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quote
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| Strict consensus will be used. |;
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else
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if (( %6 != 0.1 )||( %6 != 0.2 )||( %6 != 0.3 )||( %6!=1.1 )||( %6 !=1.2 )||( %6 !=1.3 )||( %6 != 2.1 )||( %6 != 2.2 )||( %6 != 2.3 )||( %6 != 3.1 )||( %6 != 3.2 )||( %6 != 3.3 )||( %6 != 4.1 )||( %6 != 4.2 )||( %6 != 4.3 )||( %6 != 5.1 )||( %6 != 5.2 )||( %6 != 5.3 )||( %6 != 6.1 )||( %6 != 6.2 )||( %6 != 6.3 )||( %6 != 7.1 )||( %6 != 7.2 )||( %6 != 7.3 ))
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if (!(eqstring [ %5 str ]))
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errmsg Bremer support or relative bremer support must use strict consensus;
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end
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quote
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| Strict consensus will be used. |;
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else
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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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quote
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| Majority-rule consensus will be used. |;
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else
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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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quote
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| Half strict consensus will be used. |;
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else
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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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quote
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| Strict consensus will be used. |;
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else
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errmsg %5 must be mjr hlf or str;
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end end end
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end 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 bremer support |;
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end
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if (%6==6)
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quote - | Bootstrap and bremer support |;
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end
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if (%6==7)
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quote - | Jackknifing, bootstrap and 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 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 bremer support |;
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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 - | bremer support |;
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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 - | 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 - | resampling and bremer support |;
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end
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if ( (%6>0) && (%6<1) )
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if (%6==0.1 || %6==0.3)
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quote
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| relative bremer support |;
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else
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if (%6==0.2 || %6==0.3)
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quote
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| bremer support |;
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end end
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else
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if ((%6>=1) && (%6<2))
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quote
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| Jackknifing |;
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if (%6==1.1 || %6==1.3)
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quote
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| relative bremer support |;
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else
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if (%6==1.2 || %6==1.3)
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quote
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| bremer support |;
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end end
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else
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if ((%6>=2) && (%6<3))
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quote
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| Bootstrap |;
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if (%6==2.1 || %6==2.3)
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quote
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| relative bremer support |;
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else
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if (%6==2.2 || %6==2.3)
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quote
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| bremer support |;
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end end
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else
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if ((%6>=3) && (%6<4))
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quote
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| Jackknifing and bootstrap |;
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if (%6==3.1 || %6==3.3)
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quote
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| relative bremer support |;
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else
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if (%6==3.2 || %6==3.3)
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quote
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| bremer support |;
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end end
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else
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if ((%6>=4) && (%6<5))
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quote
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| Symmetric resampling |;
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if (%6==4.1 || %6==4.3)
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quote
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| relative bremer support |;
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else
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if (%6==4.2 || %6==4.3)
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quote
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| bremer support |;
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end end
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else
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if ((%6>=5) && (%6<6))
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quote
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| Jackknifing and symmetric resampling |;
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if (%6==5.1 || %6==5.3)
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quote
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| relative bremer support |;
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else
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if (%6==5.2 || %6==5.3)
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quote
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| bremer support |;
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end end
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else
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if ((%6>=6) && (%6<7))
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quote
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| Bootstrap and symmetric resampling |;
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if (%6==6.1 || %6==6.3)
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quote
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| relative bremer support |;
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else
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if (%6==6.2 || %6==6.3)
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quote
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| bremer support |;
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end end
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else
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if ((%6>=7) && (%6<8))
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quote
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| Jackknifing, bootstrap and symmetric |
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| resampling |;
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if (%6==7.1 || %6==7.3)
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quote
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| relative bremer support |;
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else
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if (%6==7.2 || %6==7.3)
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quote
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| bremer support |;
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end end
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else
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errmsg Mistake %6 value;
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end end end end end end end 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 bremer support |;
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quote
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| relative bremer support, bremer support |
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| jackknifing, bootstrap, symmetric |
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| resampling |;
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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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quote
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| will be shown on the resample.svg. |
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| Apomorphic characters mapping will be shown |
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| on the apo.svg and saved to apo*.tre. |
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| TL, CI and RI will be calculated finally. |
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\------------------------------------------------/;
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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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else
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if (eqstring [ %3 eiw ])
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xpiwe(*;
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log %7.eiw.log;
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piwe&;
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end
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log/;
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log + %7.tnt.log;
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else
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if (eqstring [ %3 ew ])
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else
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errmsg %3 must be ew iw or eiw;
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end end end
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else
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xpiwe(*;
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log %7.eiw.log;
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piwe&;
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log/;
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log+ %7.tnt.log;
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end
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/*Search trees*/
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@ -202,11 +291,11 @@ if(argnumber>2)
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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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else
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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 1 keepall;
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end
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end end
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end
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else
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if (ntax<=74)
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@ -234,24 +323,159 @@ 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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/*Get npars number*/
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var: npars;
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set npars ntrees;
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/*Get rbr/br/jak/boot/sym support and get consensus tree*/
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ttags=;
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ttags]; /*in one line*/
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/* jak=1, boot=2, sym=4, */
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/* jak+boot=3, */
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/* jak+sym=5, boot+sym=6, */
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/* jak+boot+sym=7, */
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/* bremer=0.1, relative-bremer=0.2 */
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/* bremer+relative-bremer=0.3 */
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if (argnumber<=5)
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/*bremer search*/
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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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/*get the consensus tree number*/
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var: nsubpars;
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set nsubpars ntrees;
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/*save strict consensus tree for bremer*/
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hold+1;
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bs * 0.'nsubpars';
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/*calculate relative bremer support*/
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bs [ 0.'nsubpars' ;
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/*set the br value float*/
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macfloat 2;
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/*calculate bremer support*/
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bsupport 0.'nsubpars';
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/*choose final tree*/
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tchoose/;
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/*jakknifing*/
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resample jak replications 1000 from 0; /*from 0 will orphan other trees*/
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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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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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if(( %6 == 0.1 )||( %6 == 0.2 )||( %6 == 0.3 )||( %6==1.1 )||( %6 ==1.2 )||( %6 ==1.3 )||( %6 == 2.1 )||( %6 == 2.2 )||( %6 == 2.3 )||( %6 == 3.1 )||( %6 == 3.2 )||( %6 == 3.3 )||( %6 == 4.1 )||( %6 == 4.2 )||( %6 == 4.3 )||( %6 == 5.1 )||( %6 == 5.2 )||( %6 == 5.3 )||( %6 == 6.1 )||( %6 == 6.2 )||( %6 == 6.3 )||( %6 == 7.1 )||( %6 == 7.2 )||( %6 == 7.3 )) /*bremer support related can only use strict consensus*/
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/*bremer search*/
|
||||
sub 1; hold +1000; bbreak=fill;
|
||||
sub 3; hold +3000; bbreak=fill;
|
||||
sub 5; hold +5000; bbreak=fill;
|
||||
sub 7; hold +7000; bbreak=fill;
|
||||
|
||||
/*get the consensus tree number*/
|
||||
var: nsubpars;
|
||||
set nsubpars ntrees;
|
||||
|
||||
/*save strict consensus tree for bremer*/
|
||||
hold+1;
|
||||
bs * 0.'nsubpars';
|
||||
|
||||
if(( %6 == 0.1 )||( %6 == 0.3 )||( %6==1.1 )||( %6 ==1.3 )||( %6 == 2.1 )||( %6 == 2.3 )||( %6 == 3.1 )||( %6 == 3.3 )||( %6 == 4.1 )||( %6 == 4.3 )||( %6 == 5.1 )||( %6 == 5.3 )||( %6 == 6.1 )||( %6 == 6.3 )||( %6 == 7.1 )||( %6 == 7.3 ))
|
||||
/*calculate relative bremer support*/
|
||||
bs [ 0.'nsubpars';
|
||||
end
|
||||
|
||||
if(( %6 == 0.2 )||( %6 == 0.3 )||( %6==1.2 )||( %6 ==1.3 )||( %6 == 2.2 )||( %6 == 2.3 )||( %6 == 3.2 )||( %6 == 3.3 )||( %6 == 4.2 )||( %6 == 4.3 )||( %6 == 5.2 )||( %6 == 5.3 )||( %6 == 6.2 )||( %6 == 6.3 )||( %6 == 7.2 )||( %6 == 7.3 ))
|
||||
|
||||
/*set the br value float*/
|
||||
macfloat 2;
|
||||
|
||||
/*calculate bremer support*/
|
||||
bsupport 0.'nsubpars';
|
||||
end
|
||||
|
||||
/*choose final tree*/
|
||||
tchoose/;
|
||||
|
||||
/*jackknifing*/
|
||||
if((%6 == 1.1) || (%6 == 1.2) || (%6 == 1.3) || (%6 == 3.1) || (%6 == 3.2) || (%6 == 3.3) || (%6 == 5.1) || (%6 == 5.2) || (%6 == 5.3) || (%6 == 7.1) || (%6 == 7.2) || (%6 == 7.3))
|
||||
resample jak replications 1000 from 0;
|
||||
end
|
||||
|
||||
/*bootstrap*/
|
||||
if((%6 == 2.1) || (%6 == 2.2) || (%6 == 2.3) || (%6 == 3.1) || (%6 == 3.2) || (%6 == 3.3) || (%6 == 6.1) || (%6 == 6.2) || (%6 == 6.3) || (%6 == 7.1) || (%6 == 7.2) || (%6 == 7.3))
|
||||
resample boot replications 1000 from 0;
|
||||
end
|
||||
|
||||
/*symmetric resampling*/
|
||||
if((%6 == 4.1) || (%6 == 4.2) || (%6 == 4.3) || (%6 == 5.1) || (%6 == 5.2) || (%6 == 5.3) || (%6 == 6.1) || (%6 == 6.2) || (%6 == 6.3) || (%6 == 7.1) || (%6 == 7.2) || (%6 == 7.3))
|
||||
resample sym replications 1000 from 0;
|
||||
end
|
||||
|
||||
else /*non-bremer related should be consensus firstly*/
|
||||
|
||||
if (eqstring [ %5 str ])
|
||||
nelsen * 0.'npars';
|
||||
else
|
||||
if (eqstring [ %5 mjr ])
|
||||
majority * 0.'npars';
|
||||
else
|
||||
if (eqstring [ %5 hlf ])
|
||||
comcomp * 0.'npars';
|
||||
else
|
||||
errmsg %5 must be mjr hlf or str;
|
||||
end end end
|
||||
|
||||
/*choose the final tree: consenus tree*/
|
||||
tchoose/;
|
||||
|
||||
/*jackkinfing*/
|
||||
if((%6==1) || (%6==3) || (%6==5) || (%6==7))
|
||||
resample jak replications 1000 from 0;
|
||||
end
|
||||
|
||||
/*bootstrap*/
|
||||
if((%6==2) || (%6==3) || (%6==6) || (%6==7))
|
||||
resample boot replications 1000 from 0;
|
||||
end
|
||||
|
||||
/*symmetric resampling*/
|
||||
if((%6==4) || (%6==5) || (%6==6) || (%6==7))
|
||||
resample sym replications 1000 from 0;
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
/*Tree vault store*/
|
||||
hold /+0;
|
||||
tvault >/;
|
||||
|
||||
end
|
||||
|
||||
/*Tree vault store*/
|
||||
hold /+0;
|
||||
tvault >/;
|
||||
/*Export consensus tree with supports*/
|
||||
ttags & %7.resample.svg thickness 7 italics fontsize 15;
|
||||
log %7.resample.log;
|
||||
quote /-------------resample tags start---------------\;
|
||||
ttags/;
|
||||
quote \-------------resample tags stop----------------/;
|
||||
log/;
|
||||
log + %7.tnt.log;
|
||||
export < %7.resample.tre;
|
||||
taxname-;
|
||||
export - %7.resample_no.tre;
|
||||
ttags-;
|
||||
taxname=;
|
||||
|
||||
/*Export consensus tree*/
|
||||
tchoose /;
|
||||
|
@ -261,16 +485,33 @@ export - %7.original_no.tre;
|
|||
tsave = %7.original.ctf;
|
||||
tsave *= %7.original.tnt.tre;
|
||||
|
||||
/*Apomorphic characters*/
|
||||
export = %7.winclada.tre;
|
||||
taxname =;
|
||||
ttags=;
|
||||
apo >0;
|
||||
log %7.apo.log;
|
||||
quote /-----------apomorphy tags start --------------\;
|
||||
ttags/;
|
||||
quote \-----------apomorphy tags stop ---------------/;
|
||||
log/;
|
||||
log + %7.tnt.log;
|
||||
ttags & %7.apo.svg thickness 7 italics fontsize 15;
|
||||
export < %7.apo.tre;
|
||||
taxname-;
|
||||
export - %7.apo_no.tre;
|
||||
ttags-;
|
||||
|
||||
/*Character Analysis*/
|
||||
log %7.homo.log;
|
||||
chomo;
|
||||
cscores;
|
||||
log/;
|
||||
log + %7.tnt.log;
|
||||
|
||||
/*Caulculate TL/CI/RI score*/
|
||||
report-;
|
||||
var-;
|
||||
var =
|
||||
0 themin
|
||||
1 themax
|
||||
2 CI
|
||||
3 RI
|
||||
4 TL
|
||||
;
|
||||
var: themin themax CI RI TL ;
|
||||
set themin minsteps;
|
||||
set themax maxsteps;
|
||||
set TL length[0];
|
||||
|
@ -278,188 +519,182 @@ set CI 'themin'/'TL'; /*CI=1 means no homoplasy*/
|
|||
set RI ('themax'-'TL')/('themax'-'themin'); /*RI=1 character fits perfetcly*/
|
||||
report=;
|
||||
|
||||
/*Apomorphic characters*/
|
||||
export = %7.winclada.tre;
|
||||
taxname =;
|
||||
ttags=;
|
||||
apo >0;
|
||||
quote - /----------------------------------------------\;
|
||||
quote - apomorphy tags start ;
|
||||
ttags/;
|
||||
quote - apomorphy tags stop ;
|
||||
quote - \----------------------------------------------/;
|
||||
ttags & %7.apo.svg thickness 7 italics fontsize 15;
|
||||
export < %7.apo.tre;
|
||||
taxname-;
|
||||
export - %7.apo_no.tre;
|
||||
ttags-;
|
||||
|
||||
/*Get jak/boot/bremer support*/
|
||||
tchoose/;
|
||||
ttags=;
|
||||
ttags]; /*in one line*/
|
||||
|
||||
/* jak=1, boot=2, bremer=4, */
|
||||
/* jak+boot=3, */
|
||||
/* jak+brember=5, boot+bremer=6, */
|
||||
/* jak+boot+bremer=7, */
|
||||
/* sym=8, */
|
||||
/* jak+sym=9, boot+sym=10, bremer+sym=12 */
|
||||
/* jak+boot+sym=11, jak+bremer+sym=13, */
|
||||
/* boot+bremer+sym=14, */
|
||||
/* jak+sym+boot+bremer=15 */
|
||||
|
||||
if (argnumber<=5)
|
||||
/*jakknifing*/
|
||||
resample jak replications 1000 from 0;
|
||||
/*bootstrap*/
|
||||
resample boot replications 1000 from 0;
|
||||
/*symmetric resampling*/
|
||||
resample sym replications 1000 from 0;
|
||||
/*bremer*/
|
||||
sub 1; hold +1000; bbreak=fill;
|
||||
sub 3; hold +3000; bbreak=fill;
|
||||
sub 5; hold +5000; bbreak=fill;
|
||||
sub 7; hold +7000; bbreak=fill;
|
||||
bsupport!!0;
|
||||
else
|
||||
if((%6==1) || (%6==3) || (%6==5) || (%6==7) || (%6==9) || (%6==11) || (%6==13) || (%6==15))
|
||||
resample jak replications 1000 from 0;
|
||||
end
|
||||
|
||||
if((%6==2) || (%6==3) || (%6==6) || (%6==7) || (%6==10) || (%6==11) || (%6==14) || (%6==15))
|
||||
resample boot replications 1000 from 0;
|
||||
end
|
||||
|
||||
if((%6==8) || (%6==9) || (%6==10) || (%6==11) || (%6==12) || (%6==13) || (%6==14) || (%6==15))
|
||||
resample sym replications 1000 from 0;
|
||||
end
|
||||
|
||||
if((%6==4) || (%6==5) || (%6==6) || (%6==7) || (%6==12) || (%6==13) || (%6==14) || (%6==15))
|
||||
sub 1; hold +1000; bbreak=fill;
|
||||
sub 3; hold +3000; bbreak=fill;
|
||||
sub 5; hold +5000; bbreak=fill;
|
||||
sub 7; hold +7000; bbreak=fill;
|
||||
bsupport!!0;
|
||||
end
|
||||
end
|
||||
|
||||
/*Export consensus tree with supports*/
|
||||
ttags & %7.resample.svg thickness 7 italics fontsize 15;
|
||||
quote - /----------------------------------------------\;
|
||||
quote - resample tags start ;
|
||||
ttags/;
|
||||
quote - resample tags stop ;
|
||||
quote - \----------------------------------------------/;
|
||||
export < %7.resample.tre;
|
||||
taxname-;
|
||||
export - %7.resample_no.tre;
|
||||
ttags-;
|
||||
|
||||
/*Report CI/RI/TL */
|
||||
log %7.report.log;
|
||||
macfloat 3;
|
||||
quote Consistency Index (CI) is 'CI';
|
||||
quote Retention Index (RI) is 'RI';
|
||||
quote Tree Length (TL) is 'TL';
|
||||
log/;
|
||||
log + %7.tnt.log;
|
||||
|
||||
/*Report*/
|
||||
quote - /----------------------------------------------\;
|
||||
quote - | The analysis has been finished. |;
|
||||
quote - | The file `tnt.log` contains |;
|
||||
quote - | K, TL, CI and RI |;
|
||||
quote - | The file `trees*.tre` contain |;
|
||||
quote - | trees found by mult and xmult |;
|
||||
quote - | The file `original*.tre` contain |;
|
||||
quote - | strict consensus tree without label |;
|
||||
quote - | The file `resample*.tre` contain |;
|
||||
quote - | consensus tree with support |;
|
||||
quote - | The file `apo*.tre` contain |;
|
||||
quote - | tree with apomorphic character |;
|
||||
quote - | The file `*_no.tre` contain |;
|
||||
quote - | tree with `taxname-` |;
|
||||
quote - | The file `*.ctf` tree file is |;
|
||||
quote - | only readable for TNT |;
|
||||
quote - | The file `*.tnt.tre` contain |;
|
||||
quote - | is the ctf file with taxname |;
|
||||
quote - | The file `resample.svg` contain |;
|
||||
quote
|
||||
/----------------------------------------------\
|
||||
| The analysis has been finished. |
|
||||
| The file `tnt.log` contains |
|
||||
| K, TL, CI and RI |
|
||||
| The file `trees*.tre` contain |
|
||||
| trees found by mult and xmult |
|
||||
| The file `original*.tre` contain |
|
||||
| strict consensus tree without label |
|
||||
| The file `resample*.tre` contain |
|
||||
| consensus tree with support |
|
||||
| The file `apo*.tre` contain |
|
||||
| tree with apomorphic character |
|
||||
| The file `*_no.tre` contain |
|
||||
| tree with `taxname-` |
|
||||
| The file `*.ctf` tree file is |
|
||||
| only readable for TNT |
|
||||
| The file `*.tnt.tre` contain |
|
||||
| is the ctf file with taxname |
|
||||
| The file `resample.svg` contain |;
|
||||
|
||||
|
||||
if (argnumber>=5)
|
||||
if(eqstring [ %5 mjr ])
|
||||
quote - | majority rule consensus tree with |;
|
||||
end
|
||||
if(eqstring [ %5 hlf ])
|
||||
quote - | half strict consensus tree with |;
|
||||
end
|
||||
if (argnumber<=5)
|
||||
quote
|
||||
| strict consensus tree with |;
|
||||
else
|
||||
if ( (argnumber >=6) && (( %6 == 0.1 )||( %6 == 0.2 )||( %6 == 0.3 )||( %6==1.1 )||( %6 ==1.2 )||( %6 ==1.3 )||( %6 == 2.1 )||( %6 == 2.2 )||( %6 == 2.3 )||( %6 == 3.1 )||( %6 == 3.2 )||( %6 == 3.3 )||( %6 == 4.1 )||( %6 == 4.2 )||( %6 == 4.3 )||( %6 == 5.1 )||( %6 == 5.2 )||( %6 == 5.3 )||( %6 == 6.1 )||( %6 == 6.2 )||( %6 == 6.3 )||( %6 == 7.1 )||( %6 == 7.2 )||( %6 == 7.3 )) )
|
||||
quote
|
||||
| strict consensus tree with |;
|
||||
else
|
||||
if (eqstring [ %5 mjr ])
|
||||
quote
|
||||
| majority-rule consensus tree with |;
|
||||
else
|
||||
if (eqstring [ %5 hlf ])
|
||||
quote
|
||||
| half strict consensus tree with |;
|
||||
else
|
||||
if(eqstring [ %5 str ])
|
||||
quote - | strict consensus tree with |;
|
||||
end
|
||||
quote
|
||||
| strict consensus tree with |;
|
||||
else
|
||||
errmsg %5 must be mjr hlf or str;
|
||||
errmsg Bremer support or relative bremer support must use strict consensus;
|
||||
end end end
|
||||
end end
|
||||
|
||||
if (argnumber>=6)
|
||||
if ( (%6>0) && (%6<1) )
|
||||
if (%6==0.1 || %6==0.3)
|
||||
quote
|
||||
| relative bremer support |;
|
||||
else
|
||||
if (%6==0.2 || %6==0.3)
|
||||
quote
|
||||
| bremer support |;
|
||||
end end
|
||||
else
|
||||
if ((%6>=1) && (%6<2))
|
||||
if (%6==1.1 || %6==1.3)
|
||||
quote
|
||||
| relative bremer support |;
|
||||
else
|
||||
if (%6==1.2 || %6==1.3)
|
||||
quote
|
||||
| bremer support |;
|
||||
end end
|
||||
quote
|
||||
| jackknifing |;
|
||||
else
|
||||
if ((%6>=2) && (%6<3))
|
||||
if (%6==2.1 || %6==2.3)
|
||||
quote
|
||||
| relative bremer support |;
|
||||
else
|
||||
if (%6==2.2 || %6==2.3)
|
||||
quote
|
||||
| bremer support |;
|
||||
end end
|
||||
quote
|
||||
| bootstrap |;
|
||||
else
|
||||
if ((%6>=3) && (%6<4))
|
||||
if (%6==3.1 || %6==3.3)
|
||||
quote
|
||||
| relative bremer support |;
|
||||
else
|
||||
if (%6==3.2 || %6==3.3)
|
||||
quote
|
||||
| bremer support |;
|
||||
end end
|
||||
quote
|
||||
| jackknifing, bootstrap |;
|
||||
else
|
||||
if ((%6>=4) && (%6<5))
|
||||
if (%6==4.1 || %6==4.3)
|
||||
quote
|
||||
| relative bremer support |;
|
||||
else
|
||||
if (%6==4.2 || %6==4.3)
|
||||
quote
|
||||
| bremer support |;
|
||||
end end
|
||||
quote
|
||||
| symmetric resampling |;
|
||||
else
|
||||
if ((%6>=5) && (%6<6))
|
||||
if (%6==5.1 || %6==5.3)
|
||||
quote
|
||||
| relative bremer support |;
|
||||
else
|
||||
if (%6==5.2 || %6==5.3)
|
||||
quote
|
||||
| bremer support |;
|
||||
end end
|
||||
quote
|
||||
| jackknifing, symmetric resampling |;
|
||||
else
|
||||
if ((%6>=6) && (%6<7))
|
||||
if (%6==6.1 || %6==6.3)
|
||||
quote
|
||||
| relative bremer support |;
|
||||
else
|
||||
if (%6==6.2 || %6==6.3)
|
||||
quote
|
||||
| bremer support |;
|
||||
end end
|
||||
quote
|
||||
| bootstrap, symmetric resampling |;
|
||||
else
|
||||
if ((%6>=7) && (%6<8))
|
||||
if (%6==7.1 || %6==7.3)
|
||||
quote
|
||||
| relative bremer support |;
|
||||
else
|
||||
if (%6==7.2 || %6==7.3)
|
||||
quote
|
||||
| bremer support |;
|
||||
end end
|
||||
quote
|
||||
| jackknifing, bootstrap, symmetric |
|
||||
| resampling |;
|
||||
else
|
||||
errmsg Mistake %6 value;
|
||||
end end end end end end end end
|
||||
else
|
||||
quote - | strict consensus tree with |;
|
||||
quote
|
||||
| relative bremer support, bremer |
|
||||
| support, jackknifing, bootstrap, |
|
||||
| symmetric resampling |;
|
||||
end
|
||||
|
||||
if (argnumber>=6)
|
||||
if (%6==1)
|
||||
quote - | jackknifing |;
|
||||
end
|
||||
if (%6==2)
|
||||
quote - | bootstrap |;
|
||||
end
|
||||
if (%6==3)
|
||||
quote - | jackknifing and bootstrap |;
|
||||
end
|
||||
if (%6==4)
|
||||
quote - | bremer support |;
|
||||
end
|
||||
if (%6==5)
|
||||
quote - | jackknifing and bremer support |;
|
||||
end
|
||||
if (%6==6)
|
||||
quote - | bootstrap and bremer support |;
|
||||
end
|
||||
if (%6==7)
|
||||
quote - | jackknifing, bootstrap and |;
|
||||
quote - | bremer support |;
|
||||
end
|
||||
if (%6==8)
|
||||
quote - | symmetric resampling |;
|
||||
end
|
||||
if (%6==9)
|
||||
quote - | Jackknifing and symmetric resample |;
|
||||
end
|
||||
if (%6==10)
|
||||
quote - | Bootstrap and symmetric resample |;
|
||||
end
|
||||
if (%6==11)
|
||||
quote - | jackknifing, bootstrap and |;
|
||||
quote - | symmetric resample |;
|
||||
end
|
||||
if (%6==12)
|
||||
quote - | bremer support and symmetric |;
|
||||
quote - | resample |;
|
||||
end
|
||||
if (%6==13)
|
||||
quote - | Jackknifing, symmetric resample and |;
|
||||
quote - | bremer support |;
|
||||
end
|
||||
if (%6==14)
|
||||
quote - | bootstrap, symmetric resmaple and |;
|
||||
quote - | bremer support |;
|
||||
end
|
||||
if (%6==15)
|
||||
quote - | jackknifing, bootstrap, symmetric |;
|
||||
quote - | resample and bremer support |;
|
||||
end
|
||||
else
|
||||
quote - | jackknifing, bootstrap, symmetric |;
|
||||
quote - | resample and bremer support |;
|
||||
end
|
||||
|
||||
quote - | The file `apo.svg` contain the |;
|
||||
quote - | tree with apomorphy mapping |;
|
||||
quote - | The file `winclada.tre` can be |;
|
||||
quote - | converted by tnt2winclada |;
|
||||
quote - \----------------------------------------------/;
|
||||
quote
|
||||
| The file `apo.svg` contains the |
|
||||
| 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 |
|
||||
| of character homoplasy |
|
||||
| The file `eiw.log` contain the report |
|
||||
| of character concavities |
|
||||
| The file `winclada.tre` can be |
|
||||
| converted by tnt2winclada |
|
||||
\----------------------------------------------/;
|
||||
|
||||
/*Quit*/
|
||||
zzz;
|
||||
|
|
Loading…
Reference in a new issue