fix: runwincladtree.svg comment issue

3tnt.sh

@@ -0,0 +1,54 @@
+#!/bin/bash
+
+# Found TNT
+
+if [ -z "tnt" ]; then
+    echo "TNT not found"
+    exit 1
+fi
+
+# Define input data
+
+input_file=$1
+
+if [ -z "$input_file" ]; then
+    echo "Usage: $0 <input_file> <guoyi.run>"
+    exit 1
+fi
+
+# Define tnt script
+
+script_file=$2
+
+if [ -z "$script_file" ]; then
+    echo "Usage: $0 <input_file> <guoyi.run>"
+    echo "Warning: guoyi.run will be set as /usr/share/tnt/tnt_scripts/guoyi.run"
+    script_file="/usr/share/tnt/tnt_scripts/guoyi.run"
+fi
+
+
+# Define three weighting functions
+task1() {
+    echo "Equal Weighting started"
+    tnt run $script_file $input_file 3 ew 0 str 5 EW,
+    echo "Equal Weighting completed"
+}
+
+task2() {
+    echo "Implied Weighting started"
+    tnt run $script_file $input_file 3 iw 12 str 5 IW,
+    echo "Implied Weighting completed"
+}
+
+task3() {
+    echo "Extended Implied Weighting started"
+    tnt run $script_file $input_file 3 eiw 12 str 5 EIW,
+    echo "Extended Implied Weighting completed"
+}
+
+task1 
+task2
+task3 
+
+echo "All tasks completed"
+

CMakeLists.txt

@@ -1,15 +1,13 @@
 cmake_minimum_required(VERSION 3.0)
 
-project(tnt2winclada)
+project(tnt_script)
 SET( CMAKE_EXPORT_COMPILE_COMMANDS ON )
 
 set(CMAKE_CXX_STANDARD 11)
 
-add_executable(tnt2winclada tnt2winclada.cpp)
+add_subdirectory(src_tnt2winclada)
+add_subdirectory(src_tnt2figtree)
 
-target_compile_options(tnt2winclada PRIVATE -Wall -Wextra -pedantic)
-
-install(TARGETS tnt2winclada DESTINATION /usr/bin)
 install(FILES guoyi.run DESTINATION /usr/share/tnt/tnt_scripts)
-install(FILES LICENSE DESTINATION /usr/share/licenses/tnt2winclada)
-install(FILES README.md DESTINATION /usr/share/doc/tnt2winclada)
+install(FILES LICENSE DESTINATION /usr/share/licenses/tnt-guoyi-script)
+install(FILES README.md DESTINATION /usr/share/doc/tnt-guoyi-script)

README.md

@@ -1,6 +1,8 @@
-# TNT Script used by Guoyi
+# guoyi.run
 
-The TNT script follows MIT license. 
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8431529.svg)](https://doi.org/10.5281/zenodo.8431529)
+
+TNT Script for Maximum Parsimony Analysis (Phylogeny)
 
 ## Usage
 
@@ -14,11 +16,11 @@ The TNT script follows MIT license.
 
 - 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 1,000 hits to best length and stop, 10 cycles of drifting, ratchet and fusing) (ntax>=75).      
+- 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).      
 
-- Perform Strict consensus / Majority-rule consensus / Half strict consensus.            
+- Perform Strict consensus / Majority-rule consensus (without bremer support variations) / Half strict consensus (without bremer support variations).            
 
-- Calculate jackknifing (1,000 times), bootstrap (1,000 times) and Relative Bremer support.
+- Calculate relative Bremer support, jackknifing (1,000 times), bootstrap (1,000 times) and symmetric resampling (1,000 times).
 
 - Map apomorphic characters on the consensus tree.
 
@@ -35,10 +37,10 @@ tnt run guoyi.run filename datatype weight 0/K cons resample prefix;
 For Linux and Mac users
 
 ```
-tnt run guoyi.run filename datatype weight K cons resample prefix,
+tnt run guoyi.run filename datatype weight 0/K cons resample prefix,
 ```
 
-- datatpye should be `32`, `dna`, `prot`, `num`  
+- datatype should be `32`, `dna`, `prot`, `num` or any types tnt allowed 
 
   -  num=number, dna=DNA, prot=protein, 32=max number allowed (default)        
 
@@ -56,7 +58,7 @@ tnt run guoyi.run filename datatype weight K cons resample prefix,
 
 - resample should be sum of what you want
 
-  -  jak=1, boot=2, relative bremer=4 i.e. jak+boot+bremer=7 (default)       
+  -  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)       
 
 - prefix can  be empty or a string
 
@@ -66,68 +68,40 @@ tnt run guoyi.run filename datatype weight K cons resample prefix,
 
 - Results instructions are at the end of `tnt.log`.
 
-- `trees.tre`, `resample.tre` are trees with taxname.
+- `*.tre` are trees with taxname, `*_no.tre` are trees without taxname.
 
-- `trees_no.tre`, `resample_no.tre` are trees without taxname.
+- `*.tnt.tre` can be read by TNT/WinClada directly.
+
+- `*.ctf` can only be read by TNT via `shortread`.
+
+- `*.svg` is the tree file, which can be edited by [inkscape](https://inkscape.org)
+
+- `original*` is the consensus tree.
+
+- `apo.tre` is the apomorphic character mapping tree.
+
+- `resample.tre` is the consensus tree with support, which can be read by figtree after processing by tnt2figtree.
+
+- `trees*.tre` contains he MPTs, which can be read by figtree after processing by tnt2figtree.
+
+- `resample/apo.log` contains the tree tags.
+
+- `eiw.log` contains character concavities.
+
+- `homo.log` contains homoplasy report of all characters.
+
+- `report.log` contains CI RI TL.
+
+- `winclada.ss` includes data matrix and consensus tree and it can be read by winclada directly.
 
 - `winclada.tre` can be transferred to the acceptable format for WinClada by tnt2winclada and the output file can be put into Winclada with your tnt matrix file `filename` for mapping apomorphic characters and homoplasy.
 
 ## Cite
 
-Cite this script is mandatory, list me (Guoyi Zhang) in your Acknowledgements is recommended.
+Cite this script is mandatory, list me (Guoyi Zhang) in your Acknowledgements is recommended. This script follows MIT License.
 
-# TNT2WinClada
+# Further information
 
-```
-~|~|\ |~|~  ~)  |    |o._ |~| _  _| _ 
- | | \| |   /_   \/\/ || ||_|(_|(_|(_|
+To make tnt exported trees can be readable by WinClada (Nixon, 2021) and FigTree, please check tnt2winclada and tnt2figtree in this repository.
 
-MIT, Guoyi Zhang, 2023
-```
-
-## Function
-
-Convert TNT output tree file without tags and taxname, e.g. `winclada.tre` produced by TNT script, to WinClada acceptable format tree.
-
-## Compile
-
-### Linux & Unix
-
-```
-mkdir -p build && cd build
-cmake ..
-make && make install
-```
-
-### Windows
-
-```
-cl /EHsc tnt2winclada.cpp
-```
-
-## Usage
-
-```
-tnt2winclada -i ${input_file} -o ${output_file}
-```
-
-Interactive commands are also available.
-
-```
-tnt2winclada
-
-~|~|\ |~|~  ~)  |    |o._ |~| _  _| _ 
- | | \| |   /_   \/\/ || ||_|(_|(_|(_|
-TNT2WinClada
-MIT, Guoyi Zhang, 2023
-please type help to see more commands
-
-tnt2winclada> help
-help			show interactive commands help
-input <filename>	input a TNT output tree from the specified file
-output <filename>	output a winclada accessible tree file
-quit			quit the program
-exit			exit the program
-
-tnt2winclada>
-```
+runwincladtree.run can handle [wincladtree script](https://www.lillo.org.ar/phylogeny/tnt/scripts/wincladtree.run) with input file which must be $(PREFIX).winclada.ss or winclada.tree.

guoyi.run

@@ -2,40 +2,193 @@ macro=;
 
 log %7.tnt.log;
 
-/*Arguments*/
-if ( (argnumber == 0) | (argnumber >7) )
+/*primary notification*/
+if ( (argnumber == 0) || (argnumber >7) )
   silent -console;
-  quote -   /----------------------------------------------------\;
-  quote -   |        GUOYI TNT SCRIPT 2022-2023 MIT              |;
-  quote -   |        You need to give your filename              |;
-  quote -   | shell> tnt run guoyi.tnt filename, (Linux & Mac)   |;
-  quote -   | shell> tnt run guoyi.run filename(semicolon) (Win) |;
-  quote -   |        ==============================              |;
-  quote -   |        === Parameters     Details ===              |;
-  quote -   |        ==============================              |;
-  quote -   |        filename type weight K cons resamp prefix   |;
-  quote -   |          - type should be 32, dna, prot, num       |;
-  quote -   |            num=number, dna=DNA, prot=protein       |;
-  quote -   |            32=max number allowed (default)         |;
-  quote -   |          - weight should be iw, ew, eiw            |;
-  quote -   |            iw=implied weight, ew=equal weight      |;
-  quote -   |            eiw=extended implied weight (default)   |;
-  quote -   |            N.B. K of ew must followed 0 (=NA)      |;
-  quote -   |          - K is 12 (default) following Goloboff    |;
-  quote -   |            et al. 2017 (Cladistics 34: 407–437)    |;
-  quote -   |            it must more than 0                     |;
-  quote -   |          - cons should be str, mjr, hlf            |;
-  quote -   |            mjr=majority rule, hlf=half             |;
-  quote -   |            str=strict (default)                    |;
-  quote -   |          - resamp should be sum of what you want   |;
-  quote -   |            jak=1, boot=2, relative bremer=4        |;
-  quote -   |            i.e. jak+boot+bremer=7 (default)        |;
-  quote -   |          - prefix can be empty, or a string        |;
-  quote -   |            default is empty                        |;
-  quote -   \----------------------------------------------------/;
+  quote 
+/----------------------------------------------------\
+|        GUOYI TNT SCRIPT 2022-2023 MIT              |
+|        You need to give your filename              |
+| shell> tnt run guoyi.tnt filename, (Linux & Mac)   |
+| shell> tnt run guoyi.run filename(semicolon) (Win) |
+|        ==============================              |
+|        === Parameters     Details ===              |
+|        ==============================              |
+|        filename type weight K cons resamp prefix   |
+|          - filename extension must be lower case   |
+|            fasta (fas/fasta), tnt (tnt/ss), nexus  |
+|            (nex/nexus) format are allowed          |
+|          - type should be 32, dna, prot, num       |
+|            num=number, dna=DNA, prot=protein       |
+|            32=max number allowed (default)         |
+|          - weight should be iw, ew, eiw            |
+|            iw=implied weight, ew=equal weight      |
+|            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)    |
+|            it must more than 0                     |
+|          - cons should be str, mjr, hlf            |
+|            mjr=majority rule, hlf=half             |
+|            str=strict (default)                    |
+|          - resamp should be sum of what you want   |
+|            jak=1, boot=2, sym=4 relative-bremer    |
+|            (rbr)=0.1, bremer(br)=0.2               |
+|            i.e rbr+jak+boot+sym=7.1 (default)      |
+|          - prefix can be empty, or a string        |
+|            default is empty                        |
+\----------------------------------------------------/;
   proc/; 
 end
 
+/*Var for handling args*/
+var:
+  dojak doboot dosym dobrs dorbrs rsmp dobremer
+  dostr domjr dohlf contype
+  doew doiw doeiw dowt wtstring wttype
+  kvalue
+  search
+  isfas istnt isnex input;
+
+set dojak 0; set doboot 0; set dosym 0; set dobrs 0; set dorbrs 0; set rsmp 0; set dobremer 0;
+set dostr 0; set domjr 0; set dohlf 0;
+set doew 0; set doiw 0; set doeiw 0; set dowt 0; set wttype 0;
+set kvalue 12;
+set search 0;
+set isfas 0; set istnt 0; set isnex 0;
+
+goto=%0;
+
+/*Get prefix and extension of input*/
+set input $%1;
+
+/*confirm input format*/
+if ((eqstring [ $input>. fas ]) || (eqstring [ $input>. fasta ]))
+  set isfas 1;
+else
+if ((eqstring [ $input>. tnt ]) || (eqstring [ $input>. ss ]))
+  set istnt 1;
+else
+if ((eqstring [ $input>. nex ]) || (eqstring [ $input>. nexus ]))
+  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
+
+/*handle weighting type*/
+if (argnumber>=3)
+  set wtstring $%3;
+  if (eqstring [ $wtstring ew ])
+    set doew 1;
+    set wttype 1;
+  else
+  if (eqstring [ $wtstring iw ])
+    set doiw 1;
+    set wttype 2;
+  else
+  if (eqstring [ $wtstring eiw ])
+    set doeiw 1;
+    set wttype 3;
+  else
+   goto wttypeerr;
+  end end end
+else
+  set doeiw 1;
+  set wttype 3;
+end
+
+if ('doiw' || 'doeiw')
+  set dowt 1;
+end
+
+/*handle k value*/
+if (argnumber>=4)
+  set kvalue %4;
+  if ( 'doew' && ('kvalue' != 0))
+    goto kvalueerr;
+  end
+end
+
+/*handle resmaple type*/
+if (argnumber<6)
+  set dojak 1; set doboot 1; set dosym 1; set dorbrs 1;
+else
+  set rsmp %6;
+  loop 1 5
+    if ('rsmp' >= 4)
+      set dosym 1;
+      set rsmp 'rsmp'-4;
+    else
+    if ('rsmp' >= 2)
+      set doboot 1;
+      set rsmp 'rsmp'-2;
+    else
+    if ('rsmp' >= 1)
+      set dojak 1;
+      set rsmp 'rsmp'-1;
+    else
+    if ('rsmp' >= 0.2)
+      set dobrs 1;
+      set rsmp 'rsmp'-0.2;
+    else
+    if ('rsmp' >= 0.1)
+      set dorbrs 1;
+      set rsmp 'rsmp'-0.1;
+    end end end end end
+  stop
+end
+
+if ('rsmp' != 0)
+  errmsg Input 'rsmp' is illegal;
+end
+
+if ('dobrs' || 'dorbrs')
+  set dobremer 1;
+end
+
+/*handle consensus type*/
+if (argnumber>=6)
+  set contype $%5;
+  if ('dobremer')
+    set dostr 1;
+    if (eqstring [ $contype str ])
+    else
+    if (eqstring [ $contype mjr ])
+       goto bremererr;
+    else
+    if (eqstring [ $contype hlf ])
+      goto bremererr;
+    else
+      goto contypeerr;
+    end end end
+  else
+    if (eqstring [ $contype str ])
+      set dostr 1;
+    else
+    if (eqstring [ $contype mjr ])
+      set domjr 1;
+    else
+    if (eqstring [ $contype hlf ])
+      set dohlf 1;
+    else
+      goto contypeerr;
+    end end end
+  end
+else
+if (argnumber==5)
+  set contype $%5;
+  if ((eqstring [ $contype mjr ]) || (eqstring [ $contype hlf ]))
+    goto bremererr;
+  else
+  if (eqstring [ $contype str ])
+    set dostr 1;
+  else
+    goto contypeerr;
+  end end
+else
+  set dostr 1;
+end end
+
 /*Basic settings*/
 taxname+1000;
 taxname=;
@@ -47,170 +200,229 @@ else
 end
 nstates NOGAPS;
 
-/*Set K*/
-if(argnumber>2 )
-  if (eqstring [ %3 ew ])
-    quote Equal weighting is used;
-    if (argnumber>=4)
-      if (%4!=0)
-        quote Warning: equal weighting %4 should be fullfilled with 0;
-      end
-    end	
-  end
-  if ((eqstring [ %3 iw ]) | (eqstring [ %3 eiw ]))
-    if (argnumber>=4)
-      piwe=%4;
-    else
-      piwe=12;
-    end
-  end
-else
-  piwe=12;
+/*Set K*/ 
+if ('dowt')
+  piwe='kvalue';
 end
 
 /*Reopen tnt*/
-procedure %1;
+if ('istnt' || 'isnex')
+  procedure $input;
+else
+if ('isfas')
+  procedure & $input;
+end end
 hold 10000;
 
-/*Report what will be done*/
-quote -   /-----------------------------------------------\;
-if(argnumber>2)
-  if (eqstring [ %3 iw ])
-    if (argnumber>3)
-quote -   |    Implied weighting will be used, K is %4.    |;
-    else
-quote -   |    Implied weighting will be used, K is 12.    |;
-    end
-  end
-  if (eqstring [ %3 eiw ])
-    if (argnumber>3)
-quote -   |    Ex-implied weighting will be used, K is %4. |;
-    else
-quote -   |    Ex-implied weighting will be used, K is 12. |;
-    end
-  end
-  if (eqstring [ %3 ew ])
-quote -   |    Equal weighting will be used.               |;
+/*handle search*/
+if (ntax<=24) /*taxa lower than 25 (including 25)*/
+  if ('doeiw')
+    set search 2;
+  else
+    set search 1;
   end
 else
-quote -   |    Ex-implied weighting will be used, K is 12. |;
-end
-if (ntax<=25)
-quote -   |    Implicit enumeration will be performed.     |;
-end
-if ((ntax>25) && (ntax < 75))
-quote -   |    TBR Mult will be performed.                 |;
-end
-if (ntax>=75)
-quote -   |    TBR Mult and Xmult will be performed.       |;
-end
-if (argnumber>=5)
-  if (eqstring [ %5 mjr ])
-quote -   |    Majority-rule consensus will be used.       |;
-  end
-  if (eqstring [ %5 hlf ])
-quote -   |    Half strict consensus will be used.         |;
-  end
-  if(eqstring [ %5 str ])
-quote -   |    Strict consensus will be used.              |;
+  if (ntax<74) /*taxa lower than 75 do mult*/
+    set search 2;
+  else
+    set search 3;
   end
 end
-if (argnumber<5)
-quote -   |    Strict consensus will be used.              |;
+
+/*Report what will be done*/
+quote 
+/-----------------------------------------------\;
+if ('wttype'==1)
+  quote
+|    Equal weighting will be used.               |;
+else
+if ('wttype'==2)
+  quote
+|    Implied weighting will be used, K is 'kvalue'.    |;
+else
+if ('wttype'==3)
+  quote
+|    Ex-implied weighting will be used, K is 'kvalue'. |;
+end end end
+
+if ('search'==1)
+  quote
+|    Implicit enumeration will be performed.     |;
+else
+if ('search'==2)
+  quote
+|    TBR Mult will be performed.                 |;
+else
+if ('search'==3)
+  quote
+|    Xmult will be performed.                    |;
+end end end
+
+if ('dostr')
+  quote
+|    Strict consensus will be used.              |;
+else
+if ('domjr')
+  quote
+|    Majority-rule consensus will be used.       |;
+else
+if ('dohlf')
+  quote
+|    Half strict consensus will be used.         |;
+end end end
+
+quote
+|    resample.svg will contain a tree with       |;
+if ('dorbrs')
+  quote
+|        relative bremer support                 |;
 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 -   |    Relative bremer support                     |;
-  end
-  if (%6==5)
-quote -   |    Jackknifing and relative bremer support     |;
-  end
-  if (%6==6)
-quote -   |    Bootstrap and relative bremer support       |;
-  end
-  if (%6==7)
-quote -   |    Jackknifing, bootstrap and relative bremer  |;
-  end
+if ('dobrs')
+  quote
+|        bremer support                          |;
 end
-if (argnumber<6)
-quote -   |    Jackknifing, bootstrap and relative bremer  |;
+if ('dojak')
+  quote
+|        jackknifing                             |;
 end
-quote -   |        will be shown on the resample.svg.      |;
-quote -   |    Apomorphic characters mapping will be shown |;
-quote -   |        on the apo.svg and saved to apo*.tre.   |;
-quote -   |    TL, CI and RI will be calculated finally.   |;
-quote -   \------------------------------------------------/;
+if ('doboot')
+  quote
+|        bootstrap                               |;
+end
+if ('dosym')
+  quote
+|        symmetric resampling                    |;
+end
+
+quote
+|    Apomorphic characters mapping will be shown |
+|        on the apo.svg and saved to apo*.tre.   |
+|    TL, CI and RI will be calculated finally.   |
+\------------------------------------------------/;
 
 /*Implied weighting settings*/
-if(argnumber>2)
-  if (eqstring [ %3 iw ])
-    piwe&;
-  end
-  if (eqstring [ %3 eiw ])
-    xpiwe(*;
-    piwe&;
-  end
-else
-  xpiwe(*;
+if ('doiw')
   piwe&;
-end
+else
+if ('doeiw')
+  xpiwe(*;
+  log %7.eiw.log;
+  piwe&;
+  log/;
+  log + %7.tnt.log;
+end end
 
 /*Search trees*/
-if(eqstring [ %3 ew ] | eqstring [ %3 iw ] )
-  if (ntax<=25)
-    ienum;
-  else
-    mult=replic 1000 tbr hold 1000;
-    bbreak=tbr fill;
-    if (ntax>74)
-      sect: slack 1000; 
-      xmult=hit 1000 noupdate replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
-    end
-  end
+if ('search'==1)
+  ienum;
 else
-  mult=replic 1000 tbr hold 1000;
+if ('search'==2)
+  mult=replic 1000 tbr hold 10;
+  bbreak=tbr fill;        
+else
+if ('search'==3)
+  sect: slack 40; 
+  xmult=hit 50 replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
   bbreak=tbr fill;
-  if (ntax>74)
-    sect: slack 1000;
-    xmult=hit 1000 noupdate replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
-  end
-end
+end end end
 
 /*Export trees*/
 export= %7.trees.tre;
 taxname-;
 export= %7.trees_no.tre;
+tsave *= %7.trees.tnt.tre;
 taxname=;
 tsave = %7.trees.ctf;
-tsave *= %7.trees.tnt.tre;
 
-/*Consensus tree*/
-if (argnumber<=4)
-  nelsen *;
+/*Get npars number*/
+var: npars;
+set npars ntrees;
+
+/*Get consensus tree*/
+if ('dostr')
+  nelsen * 0.'npars';
 else
-  if (eqstring [ %5 str ])
-    nelsen *;
+if ('domjr')
+  majority * 0.'npars';
+else
+if ('dohlf')
+  comcomp * 0.'npars';
+end end end
+
+/*Get the consensus tree number*/
+var: contree;
+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=;
+ttags]; /*in one line*/
+
+/*    jak=1,		boot=2,		sym=4,		*/
+/*    jak+boot=3,					*/
+/*    jak+sym=5,	boot+sym=6,			*/
+/*    jak+boot+sym=7,  					*/
+
+/*    relative-bremer=0.1,	bremer=0.2		*/
+/*    bremer+relative-bremer=0.3			*/
+
+if ('dobremer')
+
+  /*set value of suboptimal from most parsimony tree */
+  sub: 0;
+
+  /*calculate relative bremer support*/
+  if ('dorbrs')
+  bs ]!! 0;
   end
-  if (eqstring [ %5 mjr ])
-    majority *;
-  end
-  if (eqstring [ %5 hlf ])
-    comcomp *;
+
+  /*calculate bremer support*/
+  if ('dobrs')
+  macfloat 1; /*set the br value float*/
+  bsupport !! 0;
   end
+
+end
+  
+/*Choose final tree*/
+tv<;
+tchoose/;
+
+/*adjust to zero following Pablo Goloboff*/
+sub 0;
+
+/*jakknifing*/
+if ('dojak')
+  resample jak replications 1000 from 0; /*from 0 will orphan other trees*/
 end
 
-/*Tree vault store*/
-hold /+0;
-tvault >/;
+/*bootstrap*/
+if ('doboot')
+  resample boot replications 1000 from 0;
+end
+
+/*symmetric resampling*/
+if ('dosym')
+  resample sym replications 1000 from 0;
+end
+
+/*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 /;
@@ -220,167 +432,190 @@ export - %7.original_no.tre;
 tsave = %7.original.ctf;
 tsave *= %7.original.tnt.tre;
 
-/*Caulculate TL/CI/RI score*/
-report-;
-var-;
-var =
- 0 themin
- 1 themax
- 2 CI
- 3 RI
- 4 TL
-;
-set themin minsteps;
-set themax maxsteps;
-set TL length[0];
-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                ;
+log %7.apo.log;
+quote /-----------apomorphy tags start --------------\;
 ttags/;
-quote -                     apomorphy tags stop                 ;
-quote -         \----------------------------------------------/;
+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-;
 
-/*Get jak/boot/relative-bremer support*/
-tchoose/;
-ttags=;
-ttags]; /*in one line*/
+/*Character Analysis*/
+log %7.homo.log;
+chomo;
+cscores;
+log/;
+log + %7.tnt.log;
 
-/*    jak=1,		boot=2,		bremer=4,	*/
-/*    jak+boot=3,					*/
-/*    jak+brember=5,	boot+bremer=6,			*/
-/*    jak+boot+bremer=7,  				*/
-
-if (argnumber<=5)
-  /*jakknifing*/
-  resample jak replications 1000 from 0;
-  /*bootstrap*/
-  resample boot replications 1000 from 0;
-  /*relative 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[;
-else
-  if((%6==1) | (%6==3) | (%6==5) | (%6==7))
-    resample jak replications 1000 from 0;
-  end
-  
-  if((%6==2) | (%6==3) | (%6==6) | (%6==7))
-    resample boot replications 1000 from 0;
-  end
-  
-  if((%6==4) | (%6==5) | (%6==6) | (%6==7))
-    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[;
-  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-;
+/*Caulculate TL/CI/RI score*/
+report-;
+var: themin themax CI RI TL ;
+set themin minsteps;
+set themax maxsteps;
+set TL length[0];
+set CI 'themin'/'TL'; /*CI=1 means no homoplasy*/
+set RI ('themax'-'TL')/('themax'-'themin'); /*RI=1 character fits perfetcly*/
 
 /*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/;
+
+watch-;
+/*Generate ss file for winclada*/
+log %7.winclada.ss;
+/*get basic info*/
+var: taxnum chanum;
+set taxnum ntax+1;
+set chanum nchar+1;
+/*output head*/
+quote
+xread
+'
+Data saved from TNT
+'
+'chanum' 'taxnum';
+/*outhead body*/
+xread!;
+/*output split symnol*/
+runc!
+tntprintf(";\n\n");
+!
+/*output the tread*/
+taxname-;
+tp*;
+/*output the end*/
+runc!
+tntprintf("proc/;\n");
+!
+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             |
+|          the performing details              |
+|      The file `trees*.tre` contain           |
+|          trees found by mult and xmult       |
+|      The file `original*.tre` contain        |
+|          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 tre file without 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(eqstring [ %5 str ])
-quote -         |          strict consensus tree with          |;
-  end
+if ('dostr')
+  quote
+|          strict consensus tree with          |;
 else
-quote -         |          strict consensus tree with          |;
+if ('domjr')
+  quote
+|          majority-rule consensus tree with   |;
+else
+if ('dohlf')
+  quote
+|          half strict consensus tree with     |;
+end end end
+
+if ('dorbrs')
+  quote
+|          relative bremer support             |;
+end
+if ('dobrs')
+  quote    
+|          bremer support                      |;
+end
+if ('dojak')
+  quote
+|          jackknifing                         |;
+end
+if ('doboot')
+  quote
+|          bootstrap                           |;
+end
+if ('dosym')
+  quote
+|          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 -         |          relative bremer support             |;
-  end
-  if (%6==5)
-quote -         |          jackknifing and relative bremer     |;
-quote -         |          support                             |;
-  end
-  if (%6==6)
-quote -         |          bootstrap and relative bremer       |;
-quote -         |          support                             |;
-  end
-  if (%6==7)
-quote -         |          jackknifing, bootstrap and          |;
-quote -         |          relative bremer support             |;
-  end
+if ('doew')
+  quote
+|          under equal weighting               |;
 else
-quote -         |          jackknifing, bootstrap and          |;
-quote -         |          relative bremer support             |;
+if ('doiw')
+  quote
+|          under implied weighting,            |
+|          K value is 'kvalue'                       |;
+else
+if ('doeiw')
+  quote
+|          under extended implied weighting,   |
+|          K value is 'kvalue'                       |;
+end end end
+
+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` contains    |
+|          the tree tags text                  |
+|      The file `homo.log` contains the report |
+|          of character homoplasy              |;
+
+if ('doeiw')
+quote
+|      The file `eiw.log` contains the report  |
+|          of character concavities            |;
 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 `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/;

runwincladtree.run

@@ -0,0 +1,7 @@
+macro=;
+taxname+5000;
+p %1;
+ttags=;
+apo>0;
+wincladtree %1.wincladtree.svg noalign shade rotate squaresize 15 taxangle 0;
+zzz;

src_tnt2figtree/CMakeLists.txt

@@ -0,0 +1,14 @@
+cmake_minimum_required(VERSION 3.0)
+
+project(tnt2figtree)
+SET( CMAKE_EXPORT_COMPILE_COMMANDS ON )
+
+set(CMAKE_CXX_STANDARD 11)
+
+add_executable(tnt2figtree tnt2figtree.cpp)
+
+target_compile_options(tnt2figtree PRIVATE -Wall -Wextra -pedantic)
+
+install(TARGETS tnt2figtree DESTINATION /usr/bin)
+install(FILES ../LICENSE DESTINATION /usr/share/licenses/tnt2figtree)
+install(FILES README.md DESTINATION /usr/share/doc/tnt2figtree)

src_tnt2figtree/README.md

@@ -0,0 +1,55 @@
+# TNT2FigTree
+
+```
+~|~|\ |~|~~)|~o(~|~|~._ _ _
+ | | \| | /_|~| _| | | }_}_
+
+MIT, Guoyi Zhang, 2024
+```
+
+## Function
+
+Convert TNT output tree file with resample tags, e.g. `resample.tre` produced by TNT script `guoyi.run`, to complete nexus format tree.
+
+## Compile
+
+### Linux & Unix
+
+```
+mkdir -p build && cd build
+cmake ..
+make && make install
+```
+
+### Windows
+
+```
+cl /EHsc tnt2figtree.cpp
+```
+
+## Usage
+
+```
+tnt2figtree ${input_file} ${output_file}
+```
+
+Interactive commands are also available.
+
+```
+tnt2figtree
+
+~|~|\ |~|~~)|~o(~|~|~._ _ _
+ | | \| | /_|~| _| | | }_}_
+TNT2FigTree
+MIT, Guoyi Zhang, 2024
+please type help to see more commands
+
+tnt2figtree> help
+help			show interactive commands help
+import <filename>	import a TNT output nexus format tree by TNT export command
+export <filename>	export a nexus format tree file
+quit			quit the program
+exit			exit the program
+
+tnt2figree>
+```

src_tnt2figtree/tnt2figtree.cpp

@@ -0,0 +1,198 @@
+#include <fstream>
+#include <iostream>
+#include <regex>
+#include <sstream>
+
+std::string remove_useless(std::string input_str1)
+{
+	std::string result_str1 =
+	    std::regex_replace(input_str1, std::regex(" /*"), " ");
+	result_str1 = std::regex_replace(result_str1, std::regex("\\["), "{");
+	result_str1 = std::regex_replace(result_str1, std::regex("\\]"), "}");
+	return result_str1;
+}
+
+std::string add_support(std::string input_str2)
+{
+	std::string result_str2 = "";
+	size_t i = 0;
+	while (i < input_str2.length()) {
+		if (input_str2[i] == ')') {
+			result_str2 += input_str2[i];
+			i++;
+			std::string support_str = "";
+			while (i < input_str2.length() &&
+			       std::regex_match(std::string(1, input_str2[i]),
+						std::regex("[/0-9{}?]"))) {
+				support_str += input_str2[i];
+				i++;
+			}
+			result_str2 += "[&support=\"" + support_str + "\"]";
+		}
+		else {
+			result_str2 += input_str2[i];
+			i++;
+		}
+	}
+	return result_str2;
+}
+
+std::string add_blen(std::string input_str3)
+{
+	std::string result_str3 = "";
+	int i = 0;
+	for (char c : input_str3) {
+		if (c == '(') {
+			i++;
+			result_str3 += c;
+		}
+		else if (c == ')') {
+			result_str3 += ":" + std::to_string(i) + c;
+			i--;
+		}
+		else if (c == ',') {
+			result_str3 += ":" + std::to_string(i) + c;
+		}
+		else {
+			result_str3 += c;
+		}
+	}
+	return result_str3;
+}
+
+std::string remove_slash(std::string input_str4)
+{
+	std::string result_str4 = std::regex_replace(
+	    input_str4, std::regex("\\[&support=\"[\\/\\s]*\"\\]"), "");
+	return result_str4;
+}
+
+std::vector<std::string> get_lines(std::string filename)
+{
+	std::ifstream file(filename);
+	if (!file.is_open()) {
+		std::cout << "Failed to open the input file." << std::endl;
+	}
+
+	std::vector<std::string> lines;
+	std::string line;
+	while (std::getline(file, line)) {
+		lines.push_back(line);
+	}
+	file.close();
+	return lines;
+}
+
+std::vector<std::string> process_line(std::vector<std::string> lines,
+				      size_t lineNum)
+{
+	std::string line = remove_useless(lines[lineNum]);
+	line = add_blen(line);
+	line = add_support(line);
+
+	lines[lineNum] = remove_slash(line);
+	return lines;
+}
+
+void write_lines(const std::vector<std::string>& lines,
+		 const std::string& filename)
+{
+	std::ofstream outfile(filename);
+
+	if (!outfile.is_open()) {
+		std::cout << "Failed to open the output file." << std::endl;
+	}
+
+	for (const std::string& line : lines) {
+		outfile << line << std::endl;
+	}
+
+	outfile.close();
+}
+
+void interactive_commands(std::vector<std::string> lines)
+{
+	std::string command, filename1, filename2;
+	std::cout
+	    << "~|~|\\ |~|~~)|~o(~|~|~._ _ _\n | | \\| | /_|~| _| | | }_}_"
+	    << std::endl;
+	std::cout << "TNT2FigTree\nMIT, Guoyi Zhang, 2024\nplease type help "
+		     "to see more commands"
+		  << std::endl;
+	while (true) {
+		std::cout << "tnt2figtree> ";
+		getline(std::cin, command);
+		if (command == "help") {
+			std::cout << "help\t\t\tshow interactive commands "
+				     "help\nimport <filename>\timport a TNT "
+				     "output nexus format tree by TNT export "
+				     "command\nexport <filename>\texport a "
+				     "nexus format tree file\nquit\t\t\tquit "
+				     "the program\nexit\t\t\texit the program"
+				  << std::endl;
+		}
+		else if (command.find("import ") == 0) {
+			std::stringstream ss(command.substr(7));
+			ss >> filename1;
+			if (filename1.empty()) {
+				std::cout << "tnt2figtree> please specify a "
+					     "filename."
+					  << std::endl;
+			}
+			else {
+				lines = get_lines(filename1);
+			}
+		}
+		else if (command.find("export ") == 0) {
+			std::stringstream ss(command.substr(7));
+			ss >> filename2;
+			if (filename2.empty()) {
+				std::cout << "tnt2figtree> please specify a "
+					     "filename."
+					  << std::endl;
+			}
+			else {
+				for (size_t i = 0; i < lines.size(); i++) {
+					if (lines[i][0] == '(') {
+						lines = process_line(lines, i);
+					}
+				}
+				write_lines(lines, filename2);
+			}
+		}
+		else if (command == "quit" || command == "exit") {
+			break;
+		}
+		else {
+			std::cout << "tnt2figtree> unrecognized command. Type "
+				     "'help' for "
+				     "a list of commands."
+				  << std::endl;
+		}
+	}
+}
+
+int main(int argc, char* argv[])
+{
+	std::vector<std::string> lines;
+	if (argc == 1) {
+		interactive_commands(lines);
+		return 0;
+	}
+	else if (argc == 3) {
+		lines = get_lines(argv[1]);
+		for (size_t i = 0; i < lines.size(); i++) {
+			if (lines[i][0] == '(') {
+				lines = process_line(lines, i);
+			}
+		}
+		write_lines(lines, argv[2]);
+	}
+	else {
+		std::cout << "Usage: " << argv[0]
+			  << " <input_tnt_treefile> <output_nexus_treefile>"
+			  << std::endl;
+	}
+	return 0;
+}
+

src_tnt2winclada/CMakeLists.txt

@@ -0,0 +1,14 @@
+cmake_minimum_required(VERSION 3.0)
+
+project(tnt2winclada)
+SET( CMAKE_EXPORT_COMPILE_COMMANDS ON )
+
+set(CMAKE_CXX_STANDARD 11)
+
+add_executable(tnt2winclada tnt2winclada.cpp)
+
+target_compile_options(tnt2winclada PRIVATE -Wall -Wextra -pedantic)
+
+install(TARGETS tnt2winclada DESTINATION /usr/bin)
+install(FILES ../LICENSE DESTINATION /usr/share/licenses/tnt2winclada)
+install(FILES README.md DESTINATION /usr/share/doc/tnt2winclada)

src_tnt2winclada/README.md

@@ -0,0 +1,55 @@
+# TNT2WinClada
+
+```
+~|~|\ |~|~  ~)  |    |o._ |~| _  _| _ 
+ | | \| |   /_   \/\/ || ||_|(_|(_|(_|
+
+MIT, Guoyi Zhang, 2023
+```
+
+## Function
+
+Convert TNT output tree file without tags and taxname, e.g. `winclada.tre` produced by TNT script `guoyi.run`, to WinClada acceptable format tree.
+
+## Compile
+
+### Linux & Unix
+
+```
+mkdir -p build && cd build
+cmake ..
+make && make install
+```
+
+### Windows
+
+```
+cl /EHsc tnt2winclada.cpp
+```
+
+## Usage
+
+```
+tnt2winclada -i ${input_file} -o ${output_file}
+```
+
+Interactive commands are also available.
+
+```
+tnt2winclada
+
+~|~|\ |~|~  ~)  |    |o._ |~| _  _| _ 
+ | | \| |   /_   \/\/ || ||_|(_|(_|(_|
+TNT2WinClada
+MIT, Guoyi Zhang, 2023
+please type help to see more commands
+
+tnt2winclada> help
+help			show interactive commands help
+input <filename>	input a TNT output tree from the specified file
+output <filename>	output a winclada accessible tree file
+quit			quit the program
+exit			exit the program
+
+tnt2winclada>
+```