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macro=;
log %7.tnt.log;
/*Arguments*/
if ( (argnumber == 0) || (argnumber >7) )
silent -console;
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 |
| - 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+br+jak+boot+sym=7.3 (default) |
| - prefix can be empty, or a string |
| default is empty |
\----------------------------------------------------/;
proc/;
end
/*Basic settings*/
taxname+1000;
taxname=;
mxram 10240;
if(argnumber>=2)
nstates %2;
else
nstates 32;
end
nstates NOGAPS;
/*Set K*/
if(argnumber>2 )
if (eqstring [ %3 ew ])
quote Equal weighting is used;
if ((argnumber>=4) && (%4 != 0))
errmsg equal weighting %4 should be fullfilled with 0;
end
else
if ((eqstring [ %3 iw ]) || (eqstring [ %3 eiw ]))
if (argnumber>=4)
piwe=%4;
else
piwe=12;
end
else
errmsg %3 must be ew iw or eiw;
end end
else
piwe=12;
end
/*Reopen tnt*/
procedure %1;
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
else
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
else
if (eqstring [ %3 ew ])
quote
| Equal weighting will be used. |;
else
errmsg %3 must be ew iw or eiw;
end end end
else
quote
| Ex-implied weighting will be used, K is 12. |;
end
if (ntax<=25)
quote
| Implicit enumeration will be performed. |;
else
if ((ntax>25) && (ntax < 75))
quote
| TBR Mult will be performed. |;
else
if (ntax>=75)
quote
| Xmult will be performed. |;
end end end
if (argnumber<=5)
quote
| Strict consensus will be used. |;
else
if (( %6 != 0.1 )||( %6 != 0.2 )||( %6 != 0.3 )||( %6!=1.1 )||( %6 !=1.2 )||( %6 !=1.3 )||( %6 != 2.1 )||( %6 != 2.2 )||( %6 != 2.3 )||( %6 != 3.1 )||( %6 != 3.2 )||( %6 != 3.3 )||( %6 != 4.1 )||( %6 != 4.2 )||( %6 != 4.3 )||( %6 != 5.1 )||( %6 != 5.2 )||( %6 != 5.3 )||( %6 != 6.1 )||( %6 != 6.2 )||( %6 != 6.3 )||( %6 != 7.1 )||( %6 != 7.2 )||( %6 != 7.3 ))
if (!(eqstring [ %5 str ]))
errmsg Bremer support or relative bremer support must use strict consensus;
end
quote
| Strict consensus will be used. |;
else
if (eqstring [ %5 mjr ])
quote
| Majority-rule consensus will be used. |;
else
if (eqstring [ %5 hlf ])
quote
| Half strict consensus will be used. |;
else
if(eqstring [ %5 str ])
quote
| Strict consensus will be used. |;
else
errmsg %5 must be mjr hlf or str;
end end end
end end
if (argnumber>=6)
if ( (%6>0) && (%6<1) )
if (%6==0.1 || %6==0.3)
quote
| relative bremer support |;
else
if (%6==0.2 || %6==0.3)
quote
| bremer support |;
end end
else
if ((%6>=1) && (%6<2))
quote
| Jackknifing |;
if (%6==1.1 || %6==1.3)
quote
| relative bremer support |;
else
if (%6==1.2 || %6==1.3)
quote
| bremer support |;
end end
else
if ((%6>=2) && (%6<3))
quote
| Bootstrap |;
if (%6==2.1 || %6==2.3)
quote
| relative bremer support |;
else
if (%6==2.2 || %6==2.3)
quote
| bremer support |;
end end
else
if ((%6>=3) && (%6<4))
quote
| Jackknifing and bootstrap |;
if (%6==3.1 || %6==3.3)
quote
| relative bremer support |;
else
if (%6==3.2 || %6==3.3)
quote
| bremer support |;
end end
else
if ((%6>=4) && (%6<5))
quote
| Symmetric resampling |;
if (%6==4.1 || %6==4.3)
quote
| relative bremer support |;
else
if (%6==4.2 || %6==4.3)
quote
| bremer support |;
end end
else
if ((%6>=5) && (%6<6))
quote
| Jackknifing and symmetric resampling |;
if (%6==5.1 || %6==5.3)
quote
| relative bremer support |;
else
if (%6==5.2 || %6==5.3)
quote
| bremer support |;
end end
else
if ((%6>=6) && (%6<7))
quote
| Bootstrap and symmetric resampling |;
if (%6==6.1 || %6==6.3)
quote
| relative bremer support |;
else
if (%6==6.2 || %6==6.3)
quote
| bremer support |;
end end
else
if ((%6>=7) && (%6<8))
quote
| Jackknifing, bootstrap and symmetric |
| resampling |;
if (%6==7.1 || %6==7.3)
quote
| relative bremer support |;
else
if (%6==7.2 || %6==7.3)
quote
| bremer support |;
end end
else
errmsg Mistake %6 value;
end end end end end end end end
end
if (argnumber<6)
quote
| relative bremer support, bremer support |
| jackknifing, bootstrap, symmetric |
| resampling |;
end
quote
| will be shown on the resample.svg. |
| 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&;
else
if (eqstring [ %3 eiw ])
xpiwe(*;
log %7.eiw.log;
piwe&;
log/;
log + %7.tnt.log;
else
if (eqstring [ %3 ew ])
else
errmsg %3 must be ew iw or eiw;
end end end
else
xpiwe(*;
log %7.eiw.log;
piwe&;
log/;
log+ %7.tnt.log;
end
/*Search trees*/
if(argnumber>2)
if(eqstring [ %3 ew ] || eqstring [ %3 iw ] )
if (ntax<=25)
ienum;
else
if (ntax<=74)
mult=replic 1000 tbr hold 1000;
bbreak=tbr fill;
else
if (ntax>74)
sect: slack 40;
xmult=hit 50 replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
end end
end
else
if (ntax<=74)
mult=replic 1000 tbr hold 1000;
bbreak=tbr fill;
else
sect: slack 40;
xmult=hit 50 replications 20 drift 20 ratchet 10 fuse 10 hold 1 keepall;
end
end
else
mult=replic 1000 tbr hold 1000;
bbreak=tbr fill;
if (ntax>74)
sect: slack 1000;
xmult=hit 50 replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
end
end
/*Export trees*/
export= %7.trees.tre;
taxname-;
export= %7.trees_no.tre;
taxname=;
tsave = %7.trees.ctf;
tsave *= %7.trees.tnt.tre;
/*Get npars number*/
var: npars;
set npars ntrees;
/*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, */
/* bremer=0.1, relative-bremer=0.2 */
/* bremer+relative-bremer=0.3 */
if (argnumber<=5)
/*bremer search*/
sub 1; hold +1000; bbreak=fill;
sub 3; hold +3000; bbreak=fill;
sub 5; hold +5000; bbreak=fill;
sub 7; hold +7000; bbreak=fill;
/*get the consensus tree number*/
var: nsubpars;
set nsubpars ntrees;
/*save strict consensus tree for bremer*/
hold+1;
bs * 0.'nsubpars';
/*calculate relative bremer support*/
bs [ 0.'nsubpars' ;
/*set the br value float*/
macfloat 2;
/*calculate bremer support*/
bsupport 0.'nsubpars';
/*choose final tree*/
tchoose/;
/*jakknifing*/
resample jak replications 1000 from 0; /*from 0 will orphan other trees*/
/*bootstrap*/
resample boot replications 1000 from 0;
/*symmetric resampling*/
resample sym replications 1000 from 0;
else
if(( %6 == 0.1 )||( %6 == 0.2 )||( %6 == 0.3 )||( %6==1.1 )||( %6 ==1.2 )||( %6 ==1.3 )||( %6 == 2.1 )||( %6 == 2.2 )||( %6 == 2.3 )||( %6 == 3.1 )||( %6 == 3.2 )||( %6 == 3.3 )||( %6 == 4.1 )||( %6 == 4.2 )||( %6 == 4.3 )||( %6 == 5.1 )||( %6 == 5.2 )||( %6 == 5.3 )||( %6 == 6.1 )||( %6 == 6.2 )||( %6 == 6.3 )||( %6 == 7.1 )||( %6 == 7.2 )||( %6 == 7.3 )) /*bremer support related can only use strict consensus*/
/*bremer search*/
sub 1; hold +1000; bbreak=fill;
sub 3; hold +3000; bbreak=fill;
sub 5; hold +5000; bbreak=fill;
sub 7; hold +7000; bbreak=fill;
/*get the consensus tree number*/
var: nsubpars;
set nsubpars ntrees;
/*save strict consensus tree for bremer*/
hold+1;
bs * 0.'nsubpars';
if(( %6 == 0.1 )||( %6 == 0.3 )||( %6==1.1 )||( %6 ==1.3 )||( %6 == 2.1 )||( %6 == 2.3 )||( %6 == 3.1 )||( %6 == 3.3 )||( %6 == 4.1 )||( %6 == 4.3 )||( %6 == 5.1 )||( %6 == 5.3 )||( %6 == 6.1 )||( %6 == 6.3 )||( %6 == 7.1 )||( %6 == 7.3 ))
/*calculate relative bremer support*/
bs [ 0.'nsubpars';
end
if(( %6 == 0.2 )||( %6 == 0.3 )||( %6==1.2 )||( %6 ==1.3 )||( %6 == 2.2 )||( %6 == 2.3 )||( %6 == 3.2 )||( %6 == 3.3 )||( %6 == 4.2 )||( %6 == 4.3 )||( %6 == 5.2 )||( %6 == 5.3 )||( %6 == 6.2 )||( %6 == 6.3 )||( %6 == 7.2 )||( %6 == 7.3 ))
/*set the br value float*/
macfloat 2;
/*calculate bremer support*/
bsupport 0.'nsubpars';
end
/*choose final tree*/
tchoose/;
/*jackknifing*/
if((%6 == 1.1) || (%6 == 1.2) || (%6 == 1.3) || (%6 == 3.1) || (%6 == 3.2) || (%6 == 3.3) || (%6 == 5.1) || (%6 == 5.2) || (%6 == 5.3) || (%6 == 7.1) || (%6 == 7.2) || (%6 == 7.3))
resample jak replications 1000 from 0;
end
/*bootstrap*/
if((%6 == 2.1) || (%6 == 2.2) || (%6 == 2.3) || (%6 == 3.1) || (%6 == 3.2) || (%6 == 3.3) || (%6 == 6.1) || (%6 == 6.2) || (%6 == 6.3) || (%6 == 7.1) || (%6 == 7.2) || (%6 == 7.3))
resample boot replications 1000 from 0;
end
/*symmetric resampling*/
if((%6 == 4.1) || (%6 == 4.2) || (%6 == 4.3) || (%6 == 5.1) || (%6 == 5.2) || (%6 == 5.3) || (%6 == 6.1) || (%6 == 6.2) || (%6 == 6.3) || (%6 == 7.1) || (%6 == 7.2) || (%6 == 7.3))
resample sym replications 1000 from 0;
end
else /*non-bremer related should be consensus firstly*/
if (eqstring [ %5 str ])
nelsen * 0.'npars';
else
if (eqstring [ %5 mjr ])
majority * 0.'npars';
else
if (eqstring [ %5 hlf ])
comcomp * 0.'npars';
else
errmsg %5 must be mjr hlf or str;
end end end
/*choose the final tree: consenus tree*/
tchoose/;
/*jackkinfing*/
if((%6==1) || (%6==3) || (%6==5) || (%6==7))
resample jak replications 1000 from 0;
end
/*bootstrap*/
if((%6==2) || (%6==3) || (%6==6) || (%6==7))
resample boot replications 1000 from 0;
end
/*symmetric resampling*/
if((%6==4) || (%6==5) || (%6==6) || (%6==7))
resample sym replications 1000 from 0;
end
end
/*Tree vault store*/
hold /+0;
tvault >/;
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 /;
export - %7.original.tre;
taxname-;
export - %7.original_no.tre;
tsave = %7.original.ctf;
tsave *= %7.original.tnt.tre;
/*Apomorphic characters*/
export = %7.winclada.tre;
taxname =;
ttags=;
apo >0;
log %7.apo.log;
quote /-----------apomorphy tags start --------------\;
ttags/;
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-;
/*Character Analysis*/
log %7.homo.log;
chomo;
cscores;
log/;
log + %7.tnt.log;
/*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=;
/*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/;
log + %7.tnt.log;
/*Report*/
quote
/----------------------------------------------\
| The analysis has been finished. |
| The file `tnt.log` contains |
| K, TL, CI and RI |
| The file `trees*.tre` contain |
| trees found by mult and xmult |
| The file `original*.tre` contain |
| strict 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 ctf file with taxname |
| The file `resample.svg` contain |;
if (argnumber<=5)
quote
| strict consensus tree with |;
else
if ( (argnumber >=6) && (( %6 == 0.1 )||( %6 == 0.2 )||( %6 == 0.3 )||( %6==1.1 )||( %6 ==1.2 )||( %6 ==1.3 )||( %6 == 2.1 )||( %6 == 2.2 )||( %6 == 2.3 )||( %6 == 3.1 )||( %6 == 3.2 )||( %6 == 3.3 )||( %6 == 4.1 )||( %6 == 4.2 )||( %6 == 4.3 )||( %6 == 5.1 )||( %6 == 5.2 )||( %6 == 5.3 )||( %6 == 6.1 )||( %6 == 6.2 )||( %6 == 6.3 )||( %6 == 7.1 )||( %6 == 7.2 )||( %6 == 7.3 )) )
quote
| strict consensus tree with |;
else
if (eqstring [ %5 mjr ])
quote
| majority-rule consensus tree with |;
else
if (eqstring [ %5 hlf ])
quote
| half strict consensus tree with |;
else
if(eqstring [ %5 str ])
quote
| strict consensus tree with |;
else
errmsg %5 must be mjr hlf or str;
errmsg Bremer support or relative bremer support must use strict consensus;
end end end
end end
if (argnumber>=6)
if ( (%6>0) && (%6<1) )
if (%6==0.1 || %6==0.3)
quote
| relative bremer support |;
else
if (%6==0.2 || %6==0.3)
quote
| bremer support |;
end end
else
if ((%6>=1) && (%6<2))
if (%6==1.1 || %6==1.3)
quote
| relative bremer support |;
else
if (%6==1.2 || %6==1.3)
quote
| bremer support |;
end end
quote
| jackknifing |;
else
if ((%6>=2) && (%6<3))
if (%6==2.1 || %6==2.3)
quote
| relative bremer support |;
else
if (%6==2.2 || %6==2.3)
quote
| bremer support |;
end end
quote
| bootstrap |;
else
if ((%6>=3) && (%6<4))
if (%6==3.1 || %6==3.3)
quote
| relative bremer support |;
else
if (%6==3.2 || %6==3.3)
quote
| bremer support |;
end end
quote
| jackknifing, bootstrap |;
else
if ((%6>=4) && (%6<5))
if (%6==4.1 || %6==4.3)
quote
| relative bremer support |;
else
if (%6==4.2 || %6==4.3)
quote
| bremer support |;
end end
quote
| symmetric resampling |;
else
if ((%6>=5) && (%6<6))
if (%6==5.1 || %6==5.3)
quote
| relative bremer support |;
else
if (%6==5.2 || %6==5.3)
quote
| bremer support |;
end end
quote
| jackknifing, symmetric resampling |;
else
if ((%6>=6) && (%6<7))
if (%6==6.1 || %6==6.3)
quote
| relative bremer support |;
else
if (%6==6.2 || %6==6.3)
quote
| bremer support |;
end end
quote
| bootstrap, symmetric resampling |;
else
if ((%6>=7) && (%6<8))
if (%6==7.1 || %6==7.3)
quote
| relative bremer support |;
else
if (%6==7.2 || %6==7.3)
quote
| bremer support |;
end end
quote
| jackknifing, bootstrap, symmetric |
| resampling |;
else
errmsg Mistake %6 value;
end end end end end end end end
else
quote
| relative bremer support, bremer |
| support, jackknifing, bootstrap, |
| symmetric resampling |;
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` contain the |
| tree tags in text |
| The file `homo.log` contain the report |
| of character homoplasy |
| The file `eiw.log` contain the report |
| of character concavities |
| The file `winclada.tre` can be |
| converted by tnt2winclada |
\----------------------------------------------/;
/*Quit*/
zzz;
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