add: prefix
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2 changed files with 38 additions and 25 deletions
14
README.md
14
README.md
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@ -18,7 +18,7 @@ The TNT script follows MIT and part of script is from setk.run belonging to Salv
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- Perform Strict consensus / Majority-rule consensus / Half strict consensus.
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- Calculate Relative Bremer support, jackknifing (1,000 times), and bootstrap (1,000 times).
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- Calculate jackknifing (1,000 times), bootstrap (1,000 times) and Relative Bremer support.
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- Map apomorphic characters on the consensus tree.
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@ -29,13 +29,13 @@ The TNT script follows MIT and part of script is from setk.run belonging to Salv
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For Windows users
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```
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tnt run guoyi.run filename datatype weight 0/K cons resample;
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tnt run guoyi.run filename datatype weight 0/K cons resample prefix;
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```
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For Linux and Mac users
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```
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tnt run guoyi.run filename datatype weight 0/K cons resample,
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tnt run guoyi.run filename datatype weight K cons resample prefix,
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```
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- datatpye should be `32`, `dna`, `prot`, `num`
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@ -46,6 +46,10 @@ tnt run guoyi.run filename datatype weight 0/K cons resample,
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- iw=implied weight, ew=equal weight, eiw=extended implied weight (default) N.B. ew must followed 0 (the K value position for ew iw and eiw)
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- K is 12 (default) following Goloboff et al. 2017 (Cladistics 34: 407–437)
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- it must more than 0
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- cons should be str, mjr, hlf
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- mjr=majority rule, hlf=half, str=strict (default)
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@ -54,6 +58,10 @@ tnt run guoyi.run filename datatype weight 0/K cons resample,
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- jak=1, boot=2, relative bremer=4 i.e. jak+boot+bremer=7 (default)
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- prefix can be empty or a string
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- default is empty
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## Results
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- Results instructions are at the end of `tnt.log`.
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49
guoyi.run
49
guoyi.run
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@ -1,9 +1,9 @@
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log tnt.log;
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macro=;
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log %7.tnt.log;
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/*Arguments*/
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if ( (argnumber == 0) | (argnumber >=7) )
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if ( (argnumber == 0) | (argnumber >7) )
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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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@ -13,20 +13,25 @@ if ( (argnumber == 0) | (argnumber >=7) )
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quote - | ============================== |;
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quote - | === Parameters Details === |;
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quote - | ============================== |;
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quote - | filename datatype weight 0/K cons resample |;
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quote - | - datatpye should be 32, dna, prot, num |;
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quote - | filename type weight K cons resamp prefix |;
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quote - | - type should be 32, dna, prot, num |;
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quote - | num=number, dna=DNA, prot=protein |;
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quote - | 32=max number allowed (default) |;
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quote - | - weight should be iw, ew, eiw |;
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quote - | iw=implied weight, ew=equal weight |;
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quote - | eiw=extended implied weight (default) |;
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quote - | N.B. ew must followed 0 |;
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quote - | N.B. K of ew must followed 0 (=NA) |;
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quote - | - K is 12 (default) following Goloboff |;
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quote - | et al. 2017 (Cladistics 34: 407–437) |;
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quote - | it must more than 0 |;
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quote - | - cons should be str, mjr, hlf |;
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quote - | mjr=majority rule, hlf=half |;
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quote - | str=strict (default) |;
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quote - | - resample should be sum of what you want |;
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quote - | - resamp should be sum of what you want |;
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quote - | jak=1, boot=2, relative bremer=4 |;
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quote - | i.e. jak+boot+bremer=7 (default) |;
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quote - | - prefix can be empty, or a string |;
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quote - | default is empty |;
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quote - \----------------------------------------------------/;
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proc/;
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end
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@ -181,12 +186,12 @@ else
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end
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/*Export trees*/
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export= trees.tre;
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export= %7.trees.tre;
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taxname-;
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export= trees_no.tre;
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export= %7.trees_no.tre;
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taxname=;
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tsave = trees.ctf;
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tsave *= trees.tnt.tre;
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tsave = %7.trees.ctf;
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tsave *= %7.trees.tnt.tre;
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/*Consensus tree*/
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if (argnumber<=4)
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@ -209,11 +214,11 @@ tvault >/;
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/*Export consensus tree*/
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tchoose /;
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export - original.tre;
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export - %7.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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export - %7.original_no.tre;
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tsave = %7.original.ctf;
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tsave *= %7.original.tnt.tre;
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/*Caulculate TL/CI/RI score*/
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report-;
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@ -233,7 +238,7 @@ 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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export = winclada.tre;
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export = %7.winclada.tre;
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taxname =;
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ttags=;
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apo >0;
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@ -242,10 +247,10 @@ quote - apomorphy tags start ;
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ttags/;
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quote - apomorphy tags stop ;
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quote - \----------------------------------------------/;
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ttags & apo.svg thickness 7 italics fontsize 15;
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export < apo.tre;
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ttags & %7.apo.svg thickness 7 italics fontsize 15;
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export < %7.apo.tre;
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taxname-;
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export - apo_no.tre;
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export - %7.apo_no.tre;
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ttags-;
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/*Get jak/boot/relative-bremer support*/
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@ -288,15 +293,15 @@ else
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end
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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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ttags & %7.resample.svg thickness 7 italics fontsize 15;
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quote - /----------------------------------------------\;
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quote - resample tags start ;
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ttags/;
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quote - resample tags stop ;
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quote - \----------------------------------------------/;
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export < resample.tre;
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export < %7.resample.tre;
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taxname-;
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export - resample_no.tre;
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export - %7.resample_no.tre;
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ttags-;
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/*Report CI/RI/TL */
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