622 lines
13 KiB
Plaintext
622 lines
13 KiB
Plaintext
macro=;
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log %7.tnt.log;
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/*primary notification*/
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if ( (argnumber == 0) || (argnumber >7) )
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silent -console;
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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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| - filename extension must be lower case |
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| fasta (fas/fasta), tnt (tnt/ss), nexus |
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| (nex/nexus) format are allowed |
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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+jak+boot+sym=7.1 (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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/*Var for handling args*/
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var:
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dojak doboot dosym dobrs dorbrs rsmp dobremer
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dostr domjr dohlf contype
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doew doiw doeiw dowt wtstring wttype
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kvalue
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search
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isfas istnt isnex input;
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set dojak 0; set doboot 0; set dosym 0; set dobrs 0; set dorbrs 0; set rsmp 0; set dobremer 0;
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set dostr 0; set domjr 0; set dohlf 0;
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set doew 0; set doiw 0; set doeiw 0; set dowt 0; set wttype 0;
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set kvalue 12;
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set search 0;
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set isfas 0; set istnt 0; set isnex 0;
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goto=%0;
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/*Get prefix and extension of input*/
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set input $%1;
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/*confirm input format*/
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if ((eqstring [ $input>. fas ]) || (eqstring [ $input>. fasta ]))
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set isfas 1;
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else
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if ((eqstring [ $input>. tnt ]) || (eqstring [ $input>. ss ]))
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set istnt 1;
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else
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if ((eqstring [ $input>. nex ]) || (eqstring [ $input>. nexus ]))
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set isnex 1;
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else
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errmsg extension name of input file must be fas/fasta (for fas format), tnt/ss (for Hennig86/NONA/TNT format), nex/nexus (for nex format);
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end end end
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/*handle weighting type*/
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if (argnumber>=3)
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set wtstring $%3;
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if (eqstring [ $wtstring ew ])
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set doew 1;
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set wttype 1;
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else
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if (eqstring [ $wtstring iw ])
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set doiw 1;
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set wttype 2;
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else
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if (eqstring [ $wtstring eiw ])
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set doeiw 1;
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set wttype 3;
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else
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goto wttypeerr;
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end end end
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else
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set doeiw 1;
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set wttype 3;
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end
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if ('doiw' || 'doeiw')
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set dowt 1;
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end
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/*handle k value*/
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if (argnumber>=4)
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set kvalue %4;
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if ( 'doew' && ('kvalue' != 0))
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goto kvalueerr;
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end
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end
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/*handle resmaple type*/
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if (argnumber<6)
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set dojak 1; set doboot 1; set dosym 1; set dorbrs 1;
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else
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set rsmp %6;
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loop 1 5
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if ('rsmp' >= 4)
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set dosym 1;
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set rsmp 'rsmp'-4;
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else
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if ('rsmp' >= 2)
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set doboot 1;
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set rsmp 'rsmp'-2;
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else
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if ('rsmp' >= 1)
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set dojak 1;
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set rsmp 'rsmp'-1;
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else
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if ('rsmp' >= 0.2)
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set dobrs 1;
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set rsmp 'rsmp'-0.2;
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else
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if ('rsmp' >= 0.1)
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set dorbrs 1;
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set rsmp 'rsmp'-0.1;
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end end end end end
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stop
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end
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if ('rsmp' != 0)
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errmsg Input 'rsmp' is illegal;
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end
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if ('dobrs' || 'dorbrs')
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set dobremer 1;
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end
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/*handle consensus type*/
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if (argnumber>=6)
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set contype $%5;
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if ('dobremer')
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set dostr 1;
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if (eqstring [ $contype str ])
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else
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if (eqstring [ $contype mjr ])
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goto bremererr;
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else
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if (eqstring [ $contype hlf ])
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goto bremererr;
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else
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goto contypeerr;
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end end end
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else
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if (eqstring [ $contype str ])
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set dostr 1;
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else
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if (eqstring [ $contype mjr ])
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set domjr 1;
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else
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if (eqstring [ $contype hlf ])
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set dohlf 1;
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else
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goto contypeerr;
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end end end
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end
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else
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if (argnumber==5)
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set contype $%5;
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if ((eqstring [ $contype mjr ]) || (eqstring [ $contype hlf ]))
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goto bremererr;
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else
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if (eqstring [ $contype str ])
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set dostr 1;
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else
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goto contypeerr;
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end end
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else
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set dostr 1;
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end 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 ('dowt')
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piwe='kvalue';
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end
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/*Reopen tnt*/
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if ('istnt' || 'isnex')
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procedure $input;
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else
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if ('isfas')
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procedure & $input;
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end end
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hold 10000;
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/*handle search*/
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if (ntax<=24) /*taxa lower than 25 (including 25)*/
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if ('doeiw')
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set search 2;
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else
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set search 1;
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end
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else
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if (ntax<74) /*taxa lower than 75 do mult*/
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set search 2;
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else
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set search 3;
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end
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end
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/*Report what will be done*/
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quote
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/-----------------------------------------------\;
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if ('wttype'==1)
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quote
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| Equal weighting will be used. |;
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else
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if ('wttype'==2)
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quote
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| Implied weighting will be used, K is 'kvalue'. |;
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else
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if ('wttype'==3)
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quote
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| Ex-implied weighting will be used, K is 'kvalue'. |;
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end end end
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if ('search'==1)
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quote
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| Implicit enumeration will be performed. |;
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else
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if ('search'==2)
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quote
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| TBR Mult will be performed. |;
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else
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if ('search'==3)
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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 ('dostr')
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quote
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| Strict consensus will be used. |;
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else
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if ('domjr')
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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 ('dohlf')
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quote
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| Half strict consensus will be used. |;
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end end end
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quote
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| resample.svg will contain a tree with |;
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if ('dorbrs')
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quote
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| relative bremer support |;
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end
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if ('dobrs')
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quote
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| bremer support |;
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end
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if ('dojak')
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quote
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| jackknifing |;
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end
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if ('doboot')
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quote
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| bootstrap |;
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end
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if ('dosym')
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quote
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| symmetric resampling |;
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end
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quote
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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 ('doiw')
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piwe&;
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else
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if ('doeiw')
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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 end
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/*Search trees*/
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if ('search'==1)
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ienum;
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else
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if ('search'==2)
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mult=replic 1000 tbr hold 10;
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bbreak=tbr fill;
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else
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if ('search'==3)
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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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bbreak=tbr fill;
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end end 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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tsave *= %7.trees.tnt.tre;
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taxname=;
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tsave = %7.trees.ctf;
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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 consensus tree*/
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if ('dostr')
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nelsen * 0.'npars';
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else
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if ('domjr')
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majority * 0.'npars';
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else
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if ('dohlf')
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comcomp * 0.'npars';
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end end end
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/*Get the consensus tree number*/
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var: contree;
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set contree ntrees;
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/*Store consensus tree to tree vault*/
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hold /+0;
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tv>/;
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tchoose 0.'npars';
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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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/* relative-bremer=0.1, bremer=0.2 */
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/* bremer+relative-bremer=0.3 */
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if ('dobremer')
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/*set value of suboptimal from most parsimony tree */
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sub: 0;
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/*calculate relative bremer support*/
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if ('dorbrs')
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bs ]!! 0;
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end
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/*calculate bremer support*/
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if ('dobrs')
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macfloat 1; /*set the br value float*/
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bsupport !! 0;
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end
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end
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/*Choose final tree*/
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tv<;
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tchoose/;
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/*adjust to zero following Pablo Goloboff*/
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sub 0;
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/*jakknifing*/
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if ('dojak')
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resample jak replications 1000 from 0; /*from 0 will orphan other trees*/
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end
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/*bootstrap*/
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if ('doboot')
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resample boot replications 1000 from 0;
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end
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/*symmetric resampling*/
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if ('dosym')
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resample sym replications 1000 from 0;
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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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log %7.resample.log;
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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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log/;
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log + %7.tnt.log;
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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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taxname=;
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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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/*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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log %7.apo.log;
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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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log/;
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log + %7.tnt.log;
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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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/*Character Analysis*/
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log %7.homo.log;
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chomo;
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cscores;
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log/;
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log + %7.tnt.log;
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/*Caulculate TL/CI/RI score*/
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report-;
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var: themin themax CI RI TL ;
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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 CI/RI/TL */
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log %7.report.log;
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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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log/;
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watch-;
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/*Generate ss file for winclada*/
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log %7.winclada.ss;
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/*get basic info*/
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var: taxnum chanum;
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set taxnum ntax+1;
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set chanum nchar+1;
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/*output head*/
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quote
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xread
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'
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Data saved from TNT
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'
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'chanum' 'taxnum';
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/*outhead body*/
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xread!;
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/*output split symnol*/
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runc!
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tntprintf(";\n\n");
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!
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/*output the tread*/
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taxname-;
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tp*;
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/*output the end*/
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runc!
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tntprintf("proc/;\n");
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!
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log/;
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log + %7.tnt.log;
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/*Report*/
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quote
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/----------------------------------------------\
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| The analysis has been finished. |
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| The file `tnt.log` contains |
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| the performing details |
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| The file `trees*.tre` contain |
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| trees found by mult and xmult |
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| The file `original*.tre` contain |
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| consensus tree without label |
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| The file `resample*.tre` contain |
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| consensus tree with support |
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| The file `apo*.tre` contain |
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| tree with apomorphic character |
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| The file `*_no.tre` contain |
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| tree with `taxname-` |
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| The file `*.ctf` tree file is |
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| only readable for TNT |
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| The file `*.tnt.tre` contain |
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| is the tre file without taxname |
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| The file `resample.svg` contain |;
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if ('dostr')
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quote
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| strict consensus tree with |;
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else
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if ('domjr')
|
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quote
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| majority-rule consensus tree with |;
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else
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if ('dohlf')
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quote
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| half strict consensus tree with |;
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end end end
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if ('dorbrs')
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quote
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| relative bremer support |;
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end
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if ('dobrs')
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quote
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| bremer support |;
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end
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if ('dojak')
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quote
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| jackknifing |;
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end
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if ('doboot')
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quote
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| bootstrap |;
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end
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if ('dosym')
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quote
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| symmetric resampling |;
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end
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if ('doew')
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quote
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| under equal weighting |;
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else
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if ('doiw')
|
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quote
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| under implied weighting, |
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| K value is 'kvalue' |;
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else
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if ('doeiw')
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quote
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| under extended implied weighting, |
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| K value is 'kvalue' |;
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end end end
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quote
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| The file `apo.svg` contains the |
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| tree with apomorphy mapping |
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| The file `report.log` contains the |
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| CI RI TL publish-needed info |
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| The file `resample/apo.log` contains |
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| the tree tags text |
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| The file `homo.log` contains the report |
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| of character homoplasy |;
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if ('doeiw')
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quote
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| The file `eiw.log` contains the report |
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| of character concavities |;
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end
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|
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quote
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| The file `winclada.tre` can be |
|
||
| converted by tnt2winclada |
|
||
| The file `winclada.ss` can be read by |
|
||
| winclada directly |
|
||
\----------------------------------------------/;
|
||
|
||
/*Quit*/
|
||
zzz;
|
||
|
||
/*consensus type error*/
|
||
label contypeerr
|
||
errmsg Consensus type must be str mjr or hlf;
|
||
proc/;
|
||
|
||
/*weighting type error*/
|
||
label wttypeerr
|
||
errmsg Weighting type must be ew, iw or eiw;
|
||
proc/;
|
||
|
||
/*equal weighting k value error*/
|
||
label kvalueerr
|
||
errmsg Equal weighting (ew) must be followed with 0 instead of 'kvalue';
|
||
proc/;
|
||
|
||
/*bremer support not strict consensus error*/
|
||
label bremererr
|
||
errmsg Bremer support or any bremer support variations must use strict consensus;
|
||
proc/;
|