polish: change based Pablo Goloboff's review comments

README.md

@@ -14,7 +14,7 @@ TNT Script for Maximum Parsimony Analysis (Phylogeny)
 
 - Extended implied weighting with K value setting (default, default K=12) or implied weighting with K value setting (default K=12) or equal weighting.      
 
-- Search trees via implicit enumeration (ntax<=25, but not for eiw) or TBR Mult (1000 times) with branch swapping (25<ntax<75, also for ntax<=25 with eiw) or Mult with branch swapping and Xmult (use random sectorial searches, produce 50 hits to best length and stop, 10 cycles of drifting, ratchet and fusing) (ntax>=75).      
+- Search trees via implicit enumeration (ntax<=20, but not for eiw) or TBR Mult (1000 times) with branch swapping (20<ntax<75, also for ntax<=20 with eiw) or Mult with branch swapping and Xmult (use random sectorial searches, produce 50 hits to best length and stop, 10 cycles of drifting, ratchet and fusing) (ntax>=75). 
 
 - Perform Strict consensus / Majority-rule consensus (without bremer support variations) / Half strict consensus (without bremer support variations).            
 
@@ -56,7 +56,9 @@ tnt run guoyi.run filename datatype weight 0/K cons resample prefix,
 
 - resample should be sum of what you want
 
-  -  relative bremer support (rbrs)=0.1, bremer support (brs)=0.2, jackknifing (jak)=1, bootstrap (boot)=2, symmetric resampling (sym)=4 i.e. rbrs+jak+boot+sym=7.1 (default)       
+  -  relative bremer support (rbrs)=0.1, bremer support (brs)=0.2, jackknifing (jak)=1, bootstrap (boot)=2, symmetric resampling (sym)=4 i.e. jak+boot+sym=7 (default) 
+
+  -  Notice: Bremer related support would change the tree topology, so it should be used with caution.
 
 - prefix can  be empty or a string
 
@@ -96,7 +98,7 @@ tnt run guoyi.run filename datatype weight 0/K cons resample prefix,
 
 ## Cite
 
-Cite this script is mandatory, list me (Guoyi Zhang) in your Acknowledgements is recommended. This script follows MIT License.
+If you use this script, you **must** cite this script and cite [TNT](https://www.lillo.org.ar/phylogeny/tnt/). I kindly request that you acknowledge Guoyi Zhang in your Acknowledgements. This script follows MIT License.
 
 # Further information
 

guoyi.run

@@ -7,7 +7,7 @@ if ( (argnumber == 0) || (argnumber >7) )
   silent -console;
   quote 
 /----------------------------------------------------\
-|        GUOYI TNT SCRIPT 2022-2023 MIT              |
+|        GUOYI TNT SCRIPT 2022-2025 MIT              |
 |        You need to give your filename              |
 | shell> tnt run guoyi.tnt filename, (Linux & Mac)   |
 | shell> tnt run guoyi.run filename(semicolon) (Win) |
@@ -26,8 +26,8 @@ if ( (argnumber == 0) || (argnumber >7) )
 |            eiw=extended implied weight (default)   |
 |            N.B. K of ew must followed 0 (=NA)      |
 |          - K is 12 (default) following Goloboff    |
-|            et al. 2017 (Cladistics 34: 407–437)    |
+|            et al. 2017 (Cladistics 34: 407-437)    |
-|            it must more than 0                     |
+|            it must be more than 0                  |
 |          - cons should be str, mjr, hlf            |
 |            mjr=majority rule, hlf=half             |
 |            str=strict (default)                    |
@@ -44,8 +44,8 @@ end
 /*Var for handling args*/
 var:
   dojak doboot dosym dobrs dorbrs rsmp dobremer
-  dostr domjr dohlf contype
+  dostr domjr dohlf contype[5]
-  doew doiw doeiw dowt wtstring wttype
+  doew doiw doeiw dowt wtstring[5] wttype /*[5] limits the character number, avoid overwriting values in the next declared variable.*/
   kvalue
   search
   isfas istnt isnex input;
@@ -63,17 +63,17 @@ goto=%0;
 set input $%1;
 
 /*confirm input format*/
-if ((eqstring [ $input>. fas ]) || (eqstring [ $input>. fasta ]))
+if ((isinstring [ $input .fas ] == lenstring[ $input ] ) || (isinstring [ $input .fasta ] == lenstring[ $input ] ))
   set isfas 1;
 else
-if ((eqstring [ $input>. tnt ]) || (eqstring [ $input>. ss ]))
+if ((isinstring [ $input .tnt ] == lenstring[ $input ] ) || (isinstring [ $input .ss ] == lenstring[ $input ] ))
   set istnt 1;
 else
-if ((eqstring [ $input>. nex ]) || (eqstring [ $input>. nexus ]))
+if ((isinstring [ $input .nex ] == lenstring[ $input ] ) || (isinstring [ $input .nexus ] == lenstring[ $input ] ))
   set isnex 1;	
 else
   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);
-end end end
+xend /*multiple end, but can't be used inside loops*/
 
 /*handle weighting type*/
 if (argnumber>=3)
@@ -109,9 +109,9 @@ if (argnumber>=4)
   end
 end
 
-/*handle resmaple type*/
+/*handle resample type*/
 if (argnumber<6)
-  set dojak 1; set doboot 1; set dosym 1; set dorbrs 1;
+  set dojak 1; set doboot 1; set dosym 1; set dorbrs 0;
 else
   set rsmp %6;
   loop 1 5
@@ -192,7 +192,7 @@ end end
 /*Basic settings*/
 taxname+1000;
 taxname=;
-mxram 10240;
+mxram[; mxram*2; /*allocate twice as much RAM as TNT thinks*/
 if(argnumber>=2)
   nstates %2;
 else
@@ -215,7 +215,7 @@ end end
 hold 10000;
 
 /*handle search*/
-if (ntax<=24) /*taxa lower than 25 (including 25)*/
+if (ntax<=19) /*taxa lower than 20 (including 20)*/
   if ('doeiw')
     set search 2;
   else
@@ -243,7 +243,7 @@ else
 if ('wttype'==3)
   quote
 |    Ex-implied weighting will be used, K is 'kvalue'. |;
-end end end
+xend
 
 if ('search'==1)
   quote
@@ -256,7 +256,7 @@ else
 if ('search'==3)
   quote
 |    Xmult will be performed.                    |;
-end end end
+xend
 
 if ('dostr')
   quote
@@ -269,7 +269,7 @@ else
 if ('dohlf')
   quote
 |    Half strict consensus will be used.         |;
-end end end
+xend
 
 quote
 |    resample.svg will contain a tree with       |;
@@ -324,7 +324,7 @@ if ('search'==3)
   sect: slack 40; 
   xmult=hit 50 replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
   bbreak=tbr fill;
-end end end
+xend
 
 /*Export trees*/
 export= %7.trees.tre;
@@ -347,7 +347,7 @@ if ('domjr')
 else
 if ('dohlf')
   comcomp * 0.'npars';
-end end end
+xend
 
 /*Get the consensus tree number*/
 var: contree;
@@ -356,7 +356,6 @@ set contree ntrees;
 /*Store consensus tree to tree vault*/
 hold /+0; 
 tv>/;
-tchoose 0.'npars';
 
 /*Get rbr/br/jak/boot/sym support and get consensus tree*/
 ttags=;
@@ -372,27 +371,27 @@ ttags]; /*in one line*/
 
 if ('dobremer')
 
-  /*set value of suboptimal from most parsimony tree */
+  /*set value of suboptimal from most parsimonious tree */
   sub: 0;
 
   /*calculate relative bremer support*/
   if ('dorbrs')
-  bs *]!! 0.'npars';
+  bs ]!! 0.'npars';
   end
 
   /*calculate bremer support*/
   if ('dobrs')
   macfloat 1; /*set the br value float*/
-  bsupport *!! 0.'npars';
+  bsupport !! 0.'npars';
   end
 
 end
-  
+
 /*Choose final tree*/
 tv<;
 tchoose /;
 
-/*adjust to zero following Pablo Goloboff*/
+/*Reset suboptimal to zero (resampling will do searches!)*/
 sub 0;
 
 /*jakknifing*/
@@ -460,7 +459,7 @@ cscores;
 log/;
 log + %7.tnt.log;
 
-/*Caulculate TL/CI/RI score*/
+/*Calculate TL/CI/RI score*/
 report-;
 var: themin themax CI RI TL ;
 set themin minsteps;
@@ -468,7 +467,7 @@ set themax maxsteps;
 set TL length[0];
 set CI 'themin'/'TL'; /*CI=1 means no homoplasy*/
 if ('themax' != 'themin')
-	set RI ('themax'-'TL')/('themax'-'themin'); /*RI=1 character fits perfetcly*/
+	set RI ('themax'-'TL')/('themax'-'themin'); /*RI=1 character fits perfectly*/
 else
 	set RI 999;
 end
@@ -501,17 +500,14 @@ Data saved from TNT
 'chanum' 'taxnum';
 /*outhead body*/
 xread!;
-/*output split symnol*/
+/* finishing semicolon */
-runc!
+quote .,; /* `.,` means `;` */
-tntprintf(";\n\n");
-!
 /*output the tread*/
 taxname-;
 tp*;
-/*output the end*/
+/* finishing semicolon */
-runc!
+quote .,;
-tntprintf("proc/;\n");
+quote proc/.,;
-!
 log/;
 log + %7.tnt.log;
 
@@ -549,7 +545,11 @@ if ('dohlf')
   quote
 |          half strict consensus tree with     |;
 end end end
-
+if ('dobremer')
+  quote
+|          WARNING: bremer-related will        |
+|          WARNING: change the polytomy        |;
+end
 if ('dorbrs')
   quote
 |          relative bremer support             |;
@@ -578,12 +578,12 @@ else
 if ('doiw')
   quote
 |          under implied weighting,            |
-|          K value is 'kvalue'                       |;
+|          K value is 'kvalue'                 |;
 else
 if ('doeiw')
   quote
 |          under extended implied weighting,   |
-|          K value is 'kvalue'                       |;
+|          K value is 'kvalue'                 |;
 end end end
 
 quote