224 lines
6.3 KiB
Text
224 lines
6.3 KiB
Text
log tnt.log;
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macro=;
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taxname+1000;
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taxname=;
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mxram 10240;
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nstates 32;
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nstates NOGAPS;
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/*Arguments*/
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if ( argnumber != 1 )
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silent -console;
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quote - /-----------------------------------------------\;
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quote - | GUOYI TNT SCRIPT 2022-2023 MIT |;
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quote - | You need to give your filename |;
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quote - | tnt*> guoyi filename |;
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quote - \-----------------------------------------------/;
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proc/;
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end
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/*Report what will be done*/
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quote - /-----------------------------------------------\;
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quote - | Implied weighting will be estimated. |;
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quote - | TBR Mult and Xmult will be performed. |;
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quote - | Strict consensus will be used. |;
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quote - | Relative bremer support, jackknifing and |;
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quote - | boot will be shown on the resample.svg. |;
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quote - | Apomorphic characters mapping will be shown |;
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quote - | on the apo.svg and saved to apo*.tre. |;
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quote - | TL, CI and RI will be calculated finally. |;
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quote - \------------------------------------------------/;
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/*Set K*/
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procedure %1;
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var:
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actK
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minK
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maxK
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gVal
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a
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b
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Nval
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maxIts
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;
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if (ntax<0)
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quote There is no data;
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proc/;
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end
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/** find the value of g **/
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loop 0 nchar
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if (!isinfo[#1]) continue; end
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if (!isact[#1]) continue; end
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set a=maxsteps[#1];
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set b=minsteps[#1];
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if (('a'-'b')>'gVal')
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set gVal 'a'-'b';
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end
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stop
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quote g value: 'gVal';
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set actK 10;
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set minK 0;
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set maxK 500; /** Assume 500 as the maximum possible value of K **/
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set maxIts 0;
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/** find the best value of K **/
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loop 0 1
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quote actual k value: 'actK';
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set a 1-('actK'/('actK'+1));
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quote 'a';
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set b ('actK'/('actK'+'gVal'-1))-('actK'/('actK'+'gVal'));
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quote 'b';
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set Nval 'a'/'b';
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quote N value: 'Nval';
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if (('Nval'>14.8)&&('Nval'<15.2)) endloop; end /** N is in range **/
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if ('Nval'>15.2)
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set minK 'actK';
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else
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set maxK 'actK';
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end
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set a ('maxK'-'minK')/2;
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set actK 'minK' + 'a';
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set maxIts ++;
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if ('maxIts'==100) endloop; end /** emergency exit **/
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setloop 0;
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stop
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/** If out of emergency **/
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if ('maxIts'==100)
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quote Iterations are not finished;
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quote Best K is 'actK';
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proc /;
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end
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quote K value: 'actK' (N='Nval');
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piwe='actK';
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/*Reopen tnt*/
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procedure %1;
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hold 10000;
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/*Search trees*/
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xpiwe(*;
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mult=replic 1000 tbr hold 1000;
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sect: slack 1000;
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xmult=hit 1000 noupdate replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
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piwe&;
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/*Export trees*/
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export= trees.tre;
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taxname-;
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export= trees_no.tre;
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taxname=;
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tsave = trees.ctf;
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tsave *= trees.tnt.tre;
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/*Consensus tree*/
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bbreak=tbr;
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nelsen *;
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tchoose/;
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/*Export consensus tree*/
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export - original.tre;
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taxname-;
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export - original_no.tre;
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taxname=;
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tsave = original.ctf;
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tsave *= original.tnt.tre;
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/*Get Bremer/jak/boot support*/
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tchoose/;
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ttags=;
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sub 1; hold +1000; bbreak=fill;
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sub 2; hold +2000; bbreak=fill;
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sub 3; hold +3000; bbreak=fill;
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sub 4; hold +4000; bbreak=fill;
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sub 5; hold +5000; bbreak=fill;
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sub 6; hold +6000; bbreak=fill;
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sub 7; hold +7000; bbreak=fill;
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sub 8; hold +8000; bbreak=fill;
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bsupport[;
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resample jak replications 1000;
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resample boot replications 1000;
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/*Export consensus tree with supports*/
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ttags & resample.svg thickness 7 italics fontsize 15;
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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 < resample.tre;
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taxname-;
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export - resample_no.tre;
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/*Apomorphic characters*/
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export = winclada.tre;
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taxname =;
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ttags-;
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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 & apo.svg thickness 7 italics fontsize 15;
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export < apo.tre;
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taxname-;
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export - apo_no.tre;
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ttags-;
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/*Caulculate TL/CI/RI score*/
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length *;
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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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+ CIs [ ( ntrees + 1 ) ]
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+ RIs [ ( ntrees + 1 ) ]
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+ this
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;
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set themin minsteps;
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set themax maxsteps;
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loop 0 ntrees
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progress #1 (ntrees+1) Calculating indices...;
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set this length[#1];
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set CIs[#1] 'themin'/'this'; /*CI=1 means no homoplasy*/
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set RIs[#1] ('themax'-'this')/('themax'-'themin'); /*RI=1 character fits perfetcly*/
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stop
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progress/;
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report=;
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macfloat 3;
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maketable CIs Consistency index;
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maketable RIs Retention index;
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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 `taxaname-` |;
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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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quote - | strict consensus tree with |;
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quote - | relative bremer, jak and boot |;
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quote - | support on the tree |;
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quote - | The file `apo.svg` contain the |;
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quote - | tree with apomorphy mapping |;
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quote - | The file `winclada.tre` can be |;
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quote - | converted by tnt2winclada |;
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quote - \----------------------------------------------/;
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/*Quit*/
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zzz;
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