fix: resample score doesn't map to the tre
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parent
d4c7afd20c
commit
5a7faee66e
96
guoyi.run
96
guoyi.run
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@ -1,19 +1,15 @@
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log tnt.log;
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macro=;
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taxname+1000;
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taxname=;
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mxram 10240;
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nstates 32;
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nstates NOGAPS;
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macro=; taxname+1000; taxname=; mxram 10240; nstates 32; nstates NOGAPS;
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/*Arguments*/
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if ( argnumber != 1 )
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silent -console;
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quote - /-----------------------------------------------\;
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quote - | GUOYI TNT SCRIPT 2022-2023 MIT |;
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quote - | You need to give your filename |;
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quote - | tnt*> guoyi filename |;
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quote - \-----------------------------------------------/;
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quote - /--------------------------------------------------\;
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quote - | GUOYI TNT SCRIPT 2022-2023 MIT |;
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quote - | You need to give your filename |;
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quote - | shell> tnt run guoyi.tnt filename, (Linux & Mac) |;
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quote - | shell> tnt run guoyi.run filename; (Windows) |;
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quote - \--------------------------------------------------/;
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proc/;
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end
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@ -22,8 +18,8 @@ quote - /-----------------------------------------------\;
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quote - | Implied weighting will be estimated. |;
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quote - | TBR Mult and Xmult will be performed. |;
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quote - | Strict consensus will be used. |;
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quote - | Relative bremer support, jackknifing and |;
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quote - | boot will be shown on the resample.svg. |;
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quote - | Jackknifing, bootstrap and relative bremer |;
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quote - | will be shown on the resample.svg. |;
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quote - | Apomorphic characters mapping will be shown |;
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quote - | on the apo.svg and saved to apo*.tre. |;
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quote - | TL, CI and RI will be calculated finally. |;
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@ -37,13 +33,15 @@ piwe=12;
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procedure %1;
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hold 10000;
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/*Search trees*/
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/*Implied weighting settings*/
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xpiwe(*;
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piwe&;
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/*Search trees*/
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mult=replic 1000 tbr hold 1000;
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bbreak=tbr;
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bbreak=tbr fill;
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sect: slack 1000;
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xmult=hit 1000 noupdate replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
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piwe&;
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/*Export trees*/
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export= trees.tre;
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@ -56,16 +54,36 @@ tsave *= trees.tnt.tre;
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/*Consensus tree*/
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nelsen *;
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/*Tree vault store*/
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hold /+0;
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tvault >/;
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/*Export consensus tree*/
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tchoose/;
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tchoose /;
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export - original.tre;
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taxname-;
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export - original_no.tre;
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tsave = original.ctf;
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tsave *= original.tnt.tre;
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/*Caulculate TL/CI/RI score*/
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report-;
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var-;
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var =
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0 themin
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1 themax
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2 CI
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3 RI
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4 TL
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;
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set themin minsteps;
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set themax maxsteps;
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set TL length[0];
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set CI 'themin'/'TL'; /*CI=1 means no homoplasy*/
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set RI ('themax'-'TL')/('themax'-'themin'); /*RI=1 character fits perfetcly*/
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report=;
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/*Apomorphic characters*/
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tchoose/;
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export = winclada.tre;
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taxname =;
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ttags=;
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@ -81,20 +99,19 @@ taxname-;
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export - apo_no.tre;
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ttags-;
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/*Get Bremer/jak/boot support*/
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/*Get jak/boot/relative-bremer support*/
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tchoose/;
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ttags=;
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ttags]; /*in one line*/
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resample jak replications 1000 from 0;
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resample boot replications 1000 from 0;
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sub 1; hold +1000; bbreak=fill;
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sub 2; hold +2000; bbreak=fill;
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sub 3; hold +3000; bbreak=fill;
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sub 4; hold +4000; bbreak=fill;
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sub 5; hold +5000; bbreak=fill;
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sub 6; hold +6000; bbreak=fill;
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sub 7; hold +7000; bbreak=fill;
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sub 8; hold +8000; bbreak=fill;
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bsupport[;
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resample jak replications 1000;
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resample boot replications 1000;
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/*Export consensus tree with supports*/
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ttags & resample.svg thickness 7 italics fontsize 15;
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@ -108,30 +125,11 @@ taxname-;
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export - resample_no.tre;
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ttags-;
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/*Caulculate TL/CI/RI score*/
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length *;
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report-;
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var-;
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var =
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0 themin
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1 themax
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+ CIs [ ( ntrees + 1 ) ]
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+ RIs [ ( ntrees + 1 ) ]
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+ this
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;
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set themin minsteps;
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set themax maxsteps;
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loop 0 ntrees
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progress #1 (ntrees+1) Calculating indices...;
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set this length[#1];
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set CIs[#1] 'themin'/'this'; /*CI=1 means no homoplasy*/
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set RIs[#1] ('themax'-'this')/('themax'-'themin'); /*RI=1 character fits perfetcly*/
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stop
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progress/;
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report=;
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/*Report CI/RI/TL */
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macfloat 3;
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maketable CIs Consistency index;
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maketable RIs Retention index;
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quote Consistency Index (CI) is 'CI';
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quote Retention Index (RI) is 'RI';
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quote Tree Length (TL) is 'TL';
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/*Report*/
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quote - /----------------------------------------------\;
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@ -154,7 +152,7 @@ quote - | The file `*.tnt.tre` contain |;
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quote - | is the ctf file with taxname |;
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quote - | The file `resample.svg` contain |;
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quote - | strict consensus tree with |;
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quote - | relative bremer, jak and boot |;
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quote - | relative jak, boot and bremer |;
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quote - | support on the tree |;
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quote - | The file `apo.svg` contain the |;
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quote - | tree with apomorphy mapping |;
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