README.md

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-# TNT Script used by Guoyi
-
-These scripts follow MIT except for setk.run which belongs to Salvador Arias(Instituto Miguel Lillo, San Miguel de Tucumán, Argentina).
-
-## Usage
-
-- OS: Arch Linux;
-
-- `tnt run guoyi.run file.tnt`, `file.tnt` is your data;
-
-- Type `;` and enter;
-
-## Options
-
-- `trees.tre`, `bt.tre` are trees with taxaname;
-
-- `trees_no.tre`, `bt_no.tre` are trees without taxaname which can be put into Winclada with the `file.tnt`;
-
-- `majority` can be replaced by `nelsen`;
-
-- `boot` can be replaced by `jack`;
-

guoyi.run

@@ -1,33 +0,0 @@
-log tnt.log;
-macro=;
-taxname=;
-mxram 10240;
-nstates 32;
-nstates NOGAPS;
-
-procedure %1;
-setk.run;
-
-procedure %1;
-hold 1000;
-xpiwe(*;
-mult=replic 1000 tbr hold 1;
-xpiwe&;piwe&;
-export= trees.tre;
-taxname-;
-export= trees_no.tre;
-taxname=;
-
-bbreak=tbr;
-majority *;
-
-ttags=;
-resample boot replications 1000;
-ttags & bt.svg thickness 7 italics fontsize 15;
-export < bt.tre;
-taxname-;
-export - bt_no.tre;
-
-length *;
-stats.run;
-quit ;

setk.run

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-macro=
-
-var:
- actK
- minK
- maxK
- gVal
- a
- b
- Nval
- maxIts
-;
-
-if (ntax<0)
-  quote NO HAY DATOS!;
-  proc/;
-end
-
-set gVal 1;
-
-/* busca el valor de g */
-loop 0 nchar
-  if (!isinfo[#1]) continue; end
-  if (!isact[#1]) continue; end
-  set a=maxsteps[#1];
-  set b=minsteps[#1];
-  if (('a'-'b')>'gVal')
-    set gVal 'a'-'b';
-  end
-stop
-
-quote valor de g = 'gVal';
-
-set actK 10;
-set minK 0;
-set maxK 500; /* Asume 500 como el maximo posible valor de K */
-
-set maxIts 0;
-
-/* busca el mejor valor de K */
-loop 0 1
-  quote actual valor de k = 'actK';
-  set a 1-('actK'/('actK'+1));
-  quote 'a';
-  set b ('actK'/('actK'+'gVal'-1))-('actK'/('actK'+'gVal'));
-  quote 'b';
-  set Nval 'a'/'b';
-  quote valor de N = 'Nval';
-  if (('Nval'>14.8)&&('Nval'<15.2)) endloop; end /* N esta en el rango */
-  if ('Nval'>15.2)
-    set minK 'actK';
-  else
-    set maxK 'actK';
-  end
-  set a ('maxK'-'minK')/2;
-  set actK 'minK' + 'a';
-  set maxIts ++;
-  if ('maxIts'==100) endloop; end /* salida de emergencia */
-  setloop 0;
-stop
-
-/* Si salio de emergencia */
-if ('maxIts'==100)
-  quote NO SE TERMINARON LAS ITERACIONES;
-  quote mejor K encontrado: 'actK';
-  proc /;
-end
-
-quote Valor de K: 'actK' (N='Nval');
-piwe='actK';
-proc/;

tnt.run

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+mxram 10240 ;
+nstates 32 ;
+nstates NOGAPS ;
+
+piwe=12;
+
+procedure file.tnt ;
+log tnt.log ;
+taxname= ;
+
+hold 100000 ;
+xpiwe(*; mult=replic 1000 tbr hold 10;
+xpiwe&; piwe&;
+export= trees.tre ;
+
+bbreak=tbr ;
+majority * ;
+
+ttags= ;
+resample boot replications 1000;
+ttags & bt.svg thickness 7 italics fontsize 15;
+export < bt.tre ;
+
+length * ;
+stats.run;
+
+quit ;

winclada.run

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+mxram 10240 ;
+nstates 32 ;
+nstates NOGAPS ;
+
+piwe=12;
+
+procedure mor.tnt ;
+log winclada.log ;
+
+hold 100000 ;
+xpiwe(*; mult=replic 1000 tbr hold 10;
+xpiwe&; piwe&;
+export= treeswc.tre ;
+
+bbreak=tbr ;
+majority * ;
+
+resample boot replications 1000;
+export= btwc.tre ;
+
+length * ;
+stats.run;
+
+quit ;