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add: relative bremer support; polish: bremer related search

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kuoi 2023-10-08 21:00:10 +08:00
parent cd60624662
commit b2c852eabe
1 changed files with 548 additions and 313 deletions
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857
guoyi.run
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@ -5,41 +5,43 @@ log %7.tnt.log;
/*Arguments*/ /*Arguments*/
if ( (argnumber == 0) || (argnumber >7) ) if ( (argnumber == 0) || (argnumber >7) )
silent -console; silent -console;
quote - /----------------------------------------------------\; quote
quote - | GUOYI TNT SCRIPT 2022-2023 MIT |; /----------------------------------------------------\
quote - | You need to give your filename |; | GUOYI TNT SCRIPT 2022-2023 MIT |
quote - | shell> tnt run guoyi.tnt filename, (Linux & Mac) |; | You need to give your filename |
quote - | shell> tnt run guoyi.run filename(semicolon) (Win) |; | shell> tnt run guoyi.tnt filename, (Linux & Mac) |
quote - | ============================== |; | shell> tnt run guoyi.run filename(semicolon) (Win) |
quote - | === Parameters Details === |; | ============================== |
quote - | ============================== |; | === Parameters Details === |
quote - | filename type weight K cons resamp prefix |; | ============================== |
quote - | - type should be 32, dna, prot, num |; | filename type weight K cons resamp prefix |
quote - | num=number, dna=DNA, prot=protein |; | - type should be 32, dna, prot, num |
quote - | 32=max number allowed (default) |; | num=number, dna=DNA, prot=protein |
quote - | - weight should be iw, ew, eiw |; | 32=max number allowed (default) |
quote - | iw=implied weight, ew=equal weight |; | - weight should be iw, ew, eiw |
quote - | eiw=extended implied weight (default) |; | iw=implied weight, ew=equal weight |
quote - | N.B. K of ew must followed 0 (=NA) |; | eiw=extended implied weight (default) |
quote - | - K is 12 (default) following Goloboff |; | N.B. K of ew must followed 0 (=NA) |
quote - | et al. 2017 (Cladistics 34: 407–437) |; | - K is 12 (default) following Goloboff |
quote - | it must more than 0 |; | et al. 2017 (Cladistics 34: 407–437) |
quote - | - cons should be str, mjr, hlf |; | it must more than 0 |
quote - | mjr=majority rule, hlf=half |; | - cons should be str, mjr, hlf |
quote - | str=strict (default) |; | mjr=majority rule, hlf=half |
quote - | - resamp should be sum of what you want |; | str=strict (default) |
quote - | jak=1, boot=2, bremer=4 sym=8 |; | - resamp should be sum of what you want |
quote - | i.e. jak+boot+sym+bremer=15 (default) |; | jak=1, boot=2, sym=4 relative-bremer |
quote - | - prefix can be empty, or a string |; | (rbr)=0.1, bremer(br)=0.2 |
quote - | default is empty |; | i.e rbr+br+jak+boot+sym=7.3 (default) |
quote - \----------------------------------------------------/; | - prefix can be empty, or a string |
| default is empty |
\----------------------------------------------------/;
proc/; proc/;
end end
/*Basic settings*/ /*Basic settings*/
taxname+1000; taxname+1000;
taxname=; taxname=;
mxram 500; mxram 10240;
if(argnumber>=2) if(argnumber>=2)
nstates %2; nstates %2;
else else
@ -51,19 +53,19 @@ nstates NOGAPS;
if(argnumber>2 ) if(argnumber>2 )
if (eqstring [ %3 ew ]) if (eqstring [ %3 ew ])
quote Equal weighting is used; quote Equal weighting is used;
if (argnumber>=4) if ((argnumber>=4) && (%4 != 0))
if (%4!=0) errmsg equal weighting %4 should be fullfilled with 0;
quote Warning: equal weighting %4 should be fullfilled with 0;
end
end end
end else
if ((eqstring [ %3 iw ]) || (eqstring [ %3 eiw ])) if ((eqstring [ %3 iw ]) || (eqstring [ %3 eiw ]))
if (argnumber>=4) if (argnumber>=4)
piwe=%4; piwe=%4;
else else
piwe=12; piwe=12;
end end
end else
errmsg %3 must be ew iw or eiw;
end end
else else
piwe=12; piwe=12;
end end
@ -73,124 +75,211 @@ procedure %1;
hold 10000; hold 10000;
/*Report what will be done*/ /*Report what will be done*/
quote - /-----------------------------------------------\; quote
/-----------------------------------------------\;
if(argnumber>2) if(argnumber>2)
if (eqstring [ %3 iw ]) if (eqstring [ %3 iw ])
if (argnumber>3) if (argnumber>3)
quote - | Implied weighting will be used, K is %4. |; quote
| Implied weighting will be used, K is %4. |;
else else
quote - | Implied weighting will be used, K is 12. |; quote
| Implied weighting will be used, K is 12. |;
end end
end else
if (eqstring [ %3 eiw ]) if (eqstring [ %3 eiw ])
if (argnumber>3) if (argnumber>3)
quote - | Ex-implied weighting will be used, K is %4. |; quote
| Ex-implied weighting will be used, K is %4. |;
else else
quote - | Ex-implied weighting will be used, K is 12. |; quote
| Ex-implied weighting will be used, K is 12. |;
end end
end else
if (eqstring [ %3 ew ]) if (eqstring [ %3 ew ])
quote - | Equal weighting will be used. |; quote
end | Equal weighting will be used. |;
else
errmsg %3 must be ew iw or eiw;
end end end
else else
quote - | Ex-implied weighting will be used, K is 12. |; quote
| Ex-implied weighting will be used, K is 12. |;
end end
if (ntax<=25) if (ntax<=25)
quote - | Implicit enumeration will be performed. |; quote
end | Implicit enumeration will be performed. |;
else
if ((ntax>25) && (ntax < 75)) if ((ntax>25) && (ntax < 75))
quote - | TBR Mult will be performed. |; quote
end | TBR Mult will be performed. |;
else
if (ntax>=75) if (ntax>=75)
quote - | Xmult will be performed. |; quote
end | Xmult will be performed. |;
if (argnumber>=5) 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 ]) if (eqstring [ %5 mjr ])
quote - | Majority-rule consensus will be used. |; quote
end | Majority-rule consensus will be used. |;
else
if (eqstring [ %5 hlf ]) if (eqstring [ %5 hlf ])
quote - | Half strict consensus will be used. |; quote
end | Half strict consensus will be used. |;
else
if(eqstring [ %5 str ]) if(eqstring [ %5 str ])
quote - | Strict consensus will be used. |; quote
end | Strict consensus will be used. |;
end else
if (argnumber<5) errmsg %5 must be mjr hlf or str;
quote - | Strict consensus will be used. |; end end end
end end end
if (argnumber>=6) if (argnumber>=6)
if (%6==1) if ( (%6>0) && (%6<1) )
quote - | Jackknifing |; if (%6==0.1 || %6==0.3)
end quote
if (%6==2) | relative bremer support |;
quote - | Bootstrap |; else
end if (%6==0.2 || %6==0.3)
if (%6==3) quote
quote - | Jackknifing and bootstrap |; | bremer support |;
end end end
if (%6==4) else
quote - | Relative bremer support |; if ((%6>=1) && (%6<2))
end quote
if (%6==5) | Jackknifing |;
quote - | Jackknifing and bremer support |; if (%6==1.1 || %6==1.3)
end quote
if (%6==6) | relative bremer support |;
quote - | Bootstrap and bremer support |; else
end if (%6==1.2 || %6==1.3)
if (%6==7) quote
quote - | Jackknifing, bootstrap and bremer support |; | bremer support |;
end end end
if (%6==8) else
quote - | Symmetric resampling |; if ((%6>=2) && (%6<3))
end quote
if (%6==9) | Bootstrap |;
quote - | Jackknifing and symmetric resampling |; if (%6==2.1 || %6==2.3)
end quote
if (%6==10) | relative bremer support |;
quote - | Bootstrap and symmetric resampling |; else
end if (%6==2.2 || %6==2.3)
if (%6==11) quote
quote - | Jackknifing, bootstrap and symmetric |; | bremer support |;
quote - | resampling |; end end
end else
if (%6==12) if ((%6>=3) && (%6<4))
quote - | Symmetric resampling and bremer support |; quote
end | Jackknifing and bootstrap |;
if (%6==13) if (%6==3.1 || %6==3.3)
quote - | Jackknifing, symmetric resampling and |; quote
quote - | bremer support |; | relative bremer support |;
end else
if (%6==14) if (%6==3.2 || %6==3.3)
quote - | Bootstrap, symmetric resampling and |; quote
quote - | bremer support |; | bremer support |;
end end end
if (%6==15) else
quote - | Jackknifing, bootstrap, symmetric |; if ((%6>=4) && (%6<5))
quote - | resampling and bremer support |; quote
end | 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 end
if (argnumber<6) if (argnumber<6)
quote - | Jackknifing, bootstrap, symmetric |; quote
quote - | resampling and bremer support |; | relative bremer support, bremer support |
| jackknifing, bootstrap, symmetric |
| resampling |;
end end
quote - | will be shown on the resample.svg. |; quote
quote - | Apomorphic characters mapping will be shown |; | will be shown on the resample.svg. |
quote - | on the apo.svg and saved to apo*.tre. |; | Apomorphic characters mapping will be shown |
quote - | TL, CI and RI will be calculated finally. |; | on the apo.svg and saved to apo*.tre. |
quote - \------------------------------------------------/; | TL, CI and RI will be calculated finally. |
\------------------------------------------------/;
/*Implied weighting settings*/ /*Implied weighting settings*/
if(argnumber>2) if(argnumber>2)
if (eqstring [ %3 iw ]) if (eqstring [ %3 iw ])
piwe&; piwe&;
end else
if (eqstring [ %3 eiw ]) if (eqstring [ %3 eiw ])
xpiwe(*; xpiwe(*;
log %7.eiw.log;
piwe&; piwe&;
end log/;
log + %7.tnt.log;
else
if (eqstring [ %3 ew ])
else
errmsg %3 must be ew iw or eiw;
end end end
else else
xpiwe(*; xpiwe(*;
log %7.eiw.log;
piwe&; piwe&;
log/;
log+ %7.tnt.log;
end end
/*Search trees*/ /*Search trees*/
@ -202,11 +291,11 @@ if(argnumber>2)
if (ntax<=74) if (ntax<=74)
mult=replic 1000 tbr hold 1000; mult=replic 1000 tbr hold 1000;
bbreak=tbr fill; bbreak=tbr fill;
end else
if (ntax>74) if (ntax>74)
sect: slack 40; sect: slack 40;
xmult=hit 50 replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall; xmult=hit 50 replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
end end end
end end
else else
if (ntax<=74) if (ntax<=74)
@ -234,24 +323,159 @@ taxname=;
tsave = %7.trees.ctf; tsave = %7.trees.ctf;
tsave *= %7.trees.tnt.tre; tsave *= %7.trees.tnt.tre;
/*Consensus tree*/ /*Get npars number*/
if (argnumber<=4) var: npars;
nelsen *; 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 else
if (eqstring [ %5 str ])
nelsen *; 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*/
end
if (eqstring [ %5 mjr ]) /*bremer search*/
majority *; sub 1; hold +1000; bbreak=fill;
end sub 3; hold +3000; bbreak=fill;
if (eqstring [ %5 hlf ]) sub 5; hold +5000; bbreak=fill;
comcomp *; 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 end
/*Tree vault store*/
hold /+0;
tvault >/;
end end
/*Tree vault store*/ /*Export consensus tree with supports*/
hold /+0; ttags & %7.resample.svg thickness 7 italics fontsize 15;
tvault >/; 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*/ /*Export consensus tree*/
tchoose /; tchoose /;
@ -261,16 +485,33 @@ export - %7.original_no.tre;
tsave = %7.original.ctf; tsave = %7.original.ctf;
tsave *= %7.original.tnt.tre; 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*/ /*Caulculate TL/CI/RI score*/
report-; report-;
var-; var: themin themax CI RI TL ;
var =
0 themin
1 themax
2 CI
3 RI
4 TL
;
set themin minsteps; set themin minsteps;
set themax maxsteps; set themax maxsteps;
set TL length[0]; set TL length[0];
@ -278,188 +519,182 @@ set CI 'themin'/'TL'; /*CI=1 means no homoplasy*/
set RI ('themax'-'TL')/('themax'-'themin'); /*RI=1 character fits perfetcly*/ set RI ('themax'-'TL')/('themax'-'themin'); /*RI=1 character fits perfetcly*/
report=; report=;
/*Apomorphic characters*/
export = %7.winclada.tre;
taxname =;
ttags=;
apo >0;
quote - /----------------------------------------------\;
quote - apomorphy tags start ;
ttags/;
quote - apomorphy tags stop ;
quote - \----------------------------------------------/;
ttags & %7.apo.svg thickness 7 italics fontsize 15;
export < %7.apo.tre;
taxname-;
export - %7.apo_no.tre;
ttags-;
/*Get jak/boot/bremer support*/
tchoose/;
ttags=;
ttags]; /*in one line*/
/* jak=1, boot=2, bremer=4, */
/* jak+boot=3, */
/* jak+brember=5, boot+bremer=6, */
/* jak+boot+bremer=7, */
/* sym=8, */
/* jak+sym=9, boot+sym=10, bremer+sym=12 */
/* jak+boot+sym=11, jak+bremer+sym=13, */
/* boot+bremer+sym=14, */
/* jak+sym+boot+bremer=15 */
if (argnumber<=5)
/*jakknifing*/
resample jak replications 1000 from 0;
/*bootstrap*/
resample boot replications 1000 from 0;
/*symmetric resampling*/
resample sym replications 1000 from 0;
/*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!!0;
else
if((%6==1) || (%6==3) || (%6==5) || (%6==7) || (%6==9) || (%6==11) || (%6==13) || (%6==15))
resample jak replications 1000 from 0;
end
if((%6==2) || (%6==3) || (%6==6) || (%6==7) || (%6==10) || (%6==11) || (%6==14) || (%6==15))
resample boot replications 1000 from 0;
end
if((%6==8) || (%6==9) || (%6==10) || (%6==11) || (%6==12) || (%6==13) || (%6==14) || (%6==15))
resample sym replications 1000 from 0;
end
if((%6==4) || (%6==5) || (%6==6) || (%6==7) || (%6==12) || (%6==13) || (%6==14) || (%6==15))
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!!0;
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-;
/*Report CI/RI/TL */ /*Report CI/RI/TL */
log %7.report.log;
macfloat 3; macfloat 3;
quote Consistency Index (CI) is 'CI'; quote Consistency Index (CI) is 'CI';
quote Retention Index (RI) is 'RI'; quote Retention Index (RI) is 'RI';
quote Tree Length (TL) is 'TL'; quote Tree Length (TL) is 'TL';
log/;
log + %7.tnt.log;
/*Report*/ /*Report*/
quote - /----------------------------------------------\; quote
quote - | The analysis has been finished. |; /----------------------------------------------\
quote - | The file `tnt.log` contains |; | The analysis has been finished. |
quote - | K, TL, CI and RI |; | The file `tnt.log` contains |
quote - | The file `trees*.tre` contain |; | K, TL, CI and RI |
quote - | trees found by mult and xmult |; | The file `trees*.tre` contain |
quote - | The file `original*.tre` contain |; | trees found by mult and xmult |
quote - | strict consensus tree without label |; | The file `original*.tre` contain |
quote - | The file `resample*.tre` contain |; | strict consensus tree without label |
quote - | consensus tree with support |; | The file `resample*.tre` contain |
quote - | The file `apo*.tre` contain |; | consensus tree with support |
quote - | tree with apomorphic character |; | The file `apo*.tre` contain |
quote - | The file `*_no.tre` contain |; | tree with apomorphic character |
quote - | tree with `taxname-` |; | The file `*_no.tre` contain |
quote - | The file `*.ctf` tree file is |; | tree with `taxname-` |
quote - | only readable for TNT |; | The file `*.ctf` tree file is |
quote - | The file `*.tnt.tre` contain |; | only readable for TNT |
quote - | is the ctf file with taxname |; | The file `*.tnt.tre` contain |
quote - | The file `resample.svg` contain |; | is the ctf file with taxname |
| The file `resample.svg` contain |;
if (argnumber>=5) if (argnumber<=5)
if(eqstring [ %5 mjr ]) quote
quote - | majority rule consensus tree with |; | strict 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
else else
quote - | strict consensus tree with |; 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 )) )
end 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 (argnumber>=6)
if (%6==1) if ( (%6>0) && (%6<1) )
quote - | jackknifing |; if (%6==0.1 || %6==0.3)
end quote
if (%6==2) | relative bremer support |;
quote - | bootstrap |; else
end if (%6==0.2 || %6==0.3)
if (%6==3) quote
quote - | jackknifing and bootstrap |; | bremer support |;
end end end
if (%6==4) else
quote - | bremer support |; if ((%6>=1) && (%6<2))
end if (%6==1.1 || %6==1.3)
if (%6==5) quote
quote - | jackknifing and bremer support |; | relative bremer support |;
end else
if (%6==6) if (%6==1.2 || %6==1.3)
quote - | bootstrap and bremer support |; quote
end | bremer support |;
if (%6==7) end end
quote - | jackknifing, bootstrap and |; quote
quote - | bremer support |; | jackknifing |;
end else
if (%6==8) if ((%6>=2) && (%6<3))
quote - | symmetric resampling |; if (%6==2.1 || %6==2.3)
end quote
if (%6==9) | relative bremer support |;
quote - | Jackknifing and symmetric resample |; else
end if (%6==2.2 || %6==2.3)
if (%6==10) quote
quote - | Bootstrap and symmetric resample |; | bremer support |;
end end end
if (%6==11) quote
quote - | jackknifing, bootstrap and |; | bootstrap |;
quote - | symmetric resample |; else
end if ((%6>=3) && (%6<4))
if (%6==12) if (%6==3.1 || %6==3.3)
quote - | bremer support and symmetric |; quote
quote - | resample |; | relative bremer support |;
end else
if (%6==13) if (%6==3.2 || %6==3.3)
quote - | Jackknifing, symmetric resample and |; quote
quote - | bremer support |; | bremer support |;
end end end
if (%6==14) quote
quote - | bootstrap, symmetric resmaple and |; | jackknifing, bootstrap |;
quote - | bremer support |; else
end if ((%6>=4) && (%6<5))
if (%6==15) if (%6==4.1 || %6==4.3)
quote - | jackknifing, bootstrap, symmetric |; quote
quote - | resample and bremer support |; | relative bremer support |;
end 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 else
quote - | jackknifing, bootstrap, symmetric |; quote
quote - | resample and bremer support |; | relative bremer support, bremer |
| support, jackknifing, bootstrap, |
| symmetric resampling |;
end end
quote - | The file `apo.svg` contain the |; quote
quote - | tree with apomorphy mapping |; | The file `apo.svg` contains the |
quote - | The file `winclada.tre` can be |; | tree with apomorphy mapping |
quote - | converted by tnt2winclada |; | The file `report.log` contains the |
quote - \----------------------------------------------/; | 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*/ /*Quit*/
zzz; zzz;