add: Bremer support
This commit is contained in:
parent
53bfd967b2
commit
0a1821cb11
30
README.md
30
README.md
|
|
@ -1,30 +1,36 @@
|
|||
# TNT Script used by Guoyi
|
||||
|
||||
These scripts follow MIT except for setk.run which belongs to Salvador Arias (Instituto Miguel Lillo, San Miguel de Tucumán, Argentina).
|
||||
These scripts follow MIT, part of script is from setk.run belonging to Salvador Arias (Instituto Miguel Lillo, San Miguel de Tucumán, Argentina).
|
||||
|
||||
## Usage
|
||||
|
||||
### Method1
|
||||
- Place this script and your tnt matrix under the folder that you call `tnt` or `exe` file is placed
|
||||
|
||||
- OS: Arch Linux;
|
||||
- Enter `tnt`
|
||||
|
||||
- `tnt run guoyi.run file.tnt`, `file.tnt` is your data;
|
||||
- Enter command `guoyi filename;`
|
||||
|
||||
- Type `;` and enter;
|
||||
## Functions
|
||||
|
||||
### Method2
|
||||
- Estimated implied weighting K value.
|
||||
|
||||
- Replace `%1` with your filename;
|
||||
- Search trees via TBR Mult and Xmult.
|
||||
|
||||
- Run `tnt p guoyi.run` directly;
|
||||
- Perform Strict consensus.
|
||||
|
||||
- Calculate Relative Bremer support, jackknifing, and bootstrap.
|
||||
|
||||
- Calculate TL, CI, and RI.
|
||||
|
||||
## Options
|
||||
|
||||
- `trees.tre`, `bt.tre` are trees with taxaname;
|
||||
- Results instructions are at the end of `tnt.log`.
|
||||
|
||||
- `trees_no.tre`, `bt_no.tre` are trees without taxaname which can be put into Winclada with the `file.tnt`;
|
||||
- `con.tre`, `con.tre` are trees with taxaname.
|
||||
|
||||
- `majority` can be replaced by `nelsen`;
|
||||
- `trees_no.tre`, `bt_no.tre` are trees without taxaname which can be put into Winclada with the `file.tnt`.
|
||||
|
||||
- `boot` can be replaced by `jack`;
|
||||
- `nelsen` can be replaced by `majority`.
|
||||
|
||||
- `xmult` and `mult` replications and hold trees number can be adjusted.
|
||||
|
||||
|
|
|
|||
167
guoyi.run
167
guoyi.run
|
|
@ -5,29 +5,174 @@ mxram 10240;
|
|||
nstates 32;
|
||||
nstates NOGAPS;
|
||||
|
||||
procedure %1;
|
||||
setk.run;
|
||||
/*Arguments*/
|
||||
if ( argnumber != 1 )
|
||||
silent -console;
|
||||
quote - /-----------------------------------------------\;
|
||||
quote - | GUOYI TNT SCRIPT 2022-2023 MIT |;
|
||||
quote - | You need to give your filename |;
|
||||
quote - | tnt*> guoyi filename; |;
|
||||
quote - \-----------------------------------------------/;
|
||||
proc/;
|
||||
end
|
||||
|
||||
/*Report what will be done*/
|
||||
quote - /-----------------------------------------------\;
|
||||
quote - | Implied weighting will be estimated. |;
|
||||
quote - | TBR Mult and Xmult will be performed. |;
|
||||
quote - | Strict consensus will be used. |;
|
||||
quote - | Relative bremer support, jackknifing and |;
|
||||
quote - | bootstrap will be shown on the svg. |;
|
||||
quote - | TL, CI and RI will be calculated finally. |;
|
||||
quote - \------------------------------------------------/;
|
||||
|
||||
|
||||
/*Set K*/
|
||||
procedure %1;
|
||||
hold 1000;
|
||||
var:
|
||||
actK
|
||||
minK
|
||||
maxK
|
||||
gVal
|
||||
a
|
||||
b
|
||||
Nval
|
||||
maxIts
|
||||
;
|
||||
if (ntax<0)
|
||||
quote NO HAY DATOS!;
|
||||
proc/;
|
||||
end
|
||||
set gVal 1;
|
||||
/** busca el valor de g **/
|
||||
loop 0 nchar
|
||||
if (!isinfo[#1]) continue; end
|
||||
if (!isact[#1]) continue; end
|
||||
set a=maxsteps[#1];
|
||||
set b=minsteps[#1];
|
||||
if (('a'-'b')>'gVal')
|
||||
set gVal 'a'-'b';
|
||||
end
|
||||
stop
|
||||
quote valor de g = 'gVal';
|
||||
set actK 10;
|
||||
set minK 0;
|
||||
set maxK 500; /** Asume 500 como el maximo posible valor de K **/
|
||||
set maxIts 0;
|
||||
/** busca el mejor valor de K **/
|
||||
loop 0 1
|
||||
quote actual valor de k = 'actK';
|
||||
set a 1-('actK'/('actK'+1));
|
||||
quote 'a';
|
||||
set b ('actK'/('actK'+'gVal'-1))-('actK'/('actK'+'gVal'));
|
||||
quote 'b';
|
||||
set Nval 'a'/'b';
|
||||
quote valor de N = 'Nval';
|
||||
if (('Nval'>14.8)&&('Nval'<15.2)) endloop; end /** N esta en el rango **/
|
||||
if ('Nval'>15.2)
|
||||
set minK 'actK';
|
||||
else
|
||||
set maxK 'actK';
|
||||
end
|
||||
set a ('maxK'-'minK')/2;
|
||||
set actK 'minK' + 'a';
|
||||
set maxIts ++;
|
||||
if ('maxIts'==100) endloop; end /** salida de emergencia **/
|
||||
setloop 0;
|
||||
stop
|
||||
/** Si salio de emergencia **/
|
||||
if ('maxIts'==100)
|
||||
quote NO SE TERMINARON LAS ITERACIONES;
|
||||
quote mejor K encontrado: 'actK';
|
||||
proc /;
|
||||
end
|
||||
quote Valor de K: 'actK' (N='Nval');
|
||||
piwe='actK';
|
||||
|
||||
/*Reopen tnt*/
|
||||
procedure %1;
|
||||
hold 5000;
|
||||
|
||||
/*Search trees*/
|
||||
xpiwe(*;
|
||||
mult=replic 1000 tbr hold 1;
|
||||
mult=replic 1000 tbr hold 10;
|
||||
sect: slack 1000;
|
||||
xmult=rss hit 1000 drift 10 ratchet 10 fuse 10;
|
||||
piwe&;
|
||||
|
||||
/*Export trees*/
|
||||
export= trees.tre;
|
||||
taxname-;
|
||||
export= trees_no.tre;
|
||||
taxname=;
|
||||
|
||||
/*Consensus tree*/
|
||||
bbreak=tbr;
|
||||
majority *;
|
||||
nelsen *;
|
||||
|
||||
/*Get Bremer/jak/boot support*/
|
||||
ttags=;
|
||||
sub 1; hold +1000; bbreak=fill;
|
||||
sub 2; hold +2000; bbreak=fill;
|
||||
sub 3; hold +3000; bbreak=fill;
|
||||
sub 4; hold +4000; bbreak=fill;
|
||||
sub 5; hold +5000; bbreak=fill;
|
||||
sub 6; hold +6000; bbreak=fill;
|
||||
sub 7; hold +7000; bbreak=fill;
|
||||
sub 8; hold +8000; bbreak=fill;
|
||||
bsupport[;
|
||||
resample jak replications 1000;
|
||||
resample boot replications 1000;
|
||||
ttags & bt.svg thickness 7 italics fontsize 15;
|
||||
export < bt.tre;
|
||||
taxname-;
|
||||
export - bt_no.tre;
|
||||
|
||||
/*Export consensus tree with supports*/
|
||||
ttags & con.svg thickness 7 italics fontsize 15;
|
||||
export < con.tre;
|
||||
taxname-;
|
||||
export - con_no.tre;
|
||||
|
||||
/*Caulculate TL/CI/RI score*/
|
||||
length *;
|
||||
stats.run;
|
||||
quit ;
|
||||
report-;
|
||||
var-;
|
||||
var =
|
||||
0 themin
|
||||
1 themax
|
||||
+ CIs [ ( ntrees + 1 ) ]
|
||||
+ RIs [ ( ntrees + 1 ) ]
|
||||
+ this
|
||||
;
|
||||
set themin minsteps;
|
||||
set themax maxsteps;
|
||||
loop 0 ntrees
|
||||
progress #1 (ntrees+1) Calculating indices...;
|
||||
set this length[#1];
|
||||
set CIs[#1] 'themin'/'this'; /*CI=1 means no homoplasy*/
|
||||
set RIs[#1] ('themax'-'this')/('themax'-'themin'); /*RI=1 character fits perfetcly*/
|
||||
stop
|
||||
progress/;
|
||||
report=;
|
||||
macfloat 3;
|
||||
maketable CIs Consistency index;
|
||||
maketable RIs Retention index;
|
||||
|
||||
|
||||
/*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 `con*.tre` contain |;
|
||||
quote - | strict consensus tree |;
|
||||
quote - | The file `*_no.tre` contain |;
|
||||
quote - | tree with `taxaname-` |;
|
||||
quote - | The file `con.svg` contain |;
|
||||
quote - | strict consensus tree with |;
|
||||
quote - | relative bremer, jak and boot |;
|
||||
quote - | support on the tree |;
|
||||
quote - \----------------------------------------------/;
|
||||
|
||||
/*Quit*/
|
||||
zzz;
|
||||
|
|
|
|||
71
setk.run
71
setk.run
|
|
@ -1,71 +0,0 @@
|
|||
macro=
|
||||
|
||||
var:
|
||||
actK
|
||||
minK
|
||||
maxK
|
||||
gVal
|
||||
a
|
||||
b
|
||||
Nval
|
||||
maxIts
|
||||
;
|
||||
|
||||
if (ntax<0)
|
||||
quote NO HAY DATOS!;
|
||||
proc/;
|
||||
end
|
||||
|
||||
set gVal 1;
|
||||
|
||||
/* busca el valor de g */
|
||||
loop 0 nchar
|
||||
if (!isinfo[#1]) continue; end
|
||||
if (!isact[#1]) continue; end
|
||||
set a=maxsteps[#1];
|
||||
set b=minsteps[#1];
|
||||
if (('a'-'b')>'gVal')
|
||||
set gVal 'a'-'b';
|
||||
end
|
||||
stop
|
||||
|
||||
quote valor de g = 'gVal';
|
||||
|
||||
set actK 10;
|
||||
set minK 0;
|
||||
set maxK 500; /* Asume 500 como el maximo posible valor de K */
|
||||
|
||||
set maxIts 0;
|
||||
|
||||
/* busca el mejor valor de K */
|
||||
loop 0 1
|
||||
quote actual valor de k = 'actK';
|
||||
set a 1-('actK'/('actK'+1));
|
||||
quote 'a';
|
||||
set b ('actK'/('actK'+'gVal'-1))-('actK'/('actK'+'gVal'));
|
||||
quote 'b';
|
||||
set Nval 'a'/'b';
|
||||
quote valor de N = 'Nval';
|
||||
if (('Nval'>14.8)&&('Nval'<15.2)) endloop; end /* N esta en el rango */
|
||||
if ('Nval'>15.2)
|
||||
set minK 'actK';
|
||||
else
|
||||
set maxK 'actK';
|
||||
end
|
||||
set a ('maxK'-'minK')/2;
|
||||
set actK 'minK' + 'a';
|
||||
set maxIts ++;
|
||||
if ('maxIts'==100) endloop; end /* salida de emergencia */
|
||||
setloop 0;
|
||||
stop
|
||||
|
||||
/* Si salio de emergencia */
|
||||
if ('maxIts'==100)
|
||||
quote NO SE TERMINARON LAS ITERACIONES;
|
||||
quote mejor K encontrado: 'actK';
|
||||
proc /;
|
||||
end
|
||||
|
||||
quote Valor de K: 'actK' (N='Nval');
|
||||
piwe='actK';
|
||||
proc/;
|
||||
23
stats.run
23
stats.run
|
|
@ -1,23 +0,0 @@
|
|||
macro= ;
|
||||
report- ;
|
||||
var =
|
||||
0 themin
|
||||
1 themax
|
||||
+ CIs [ ( ntrees + 1 ) ]
|
||||
+ RIs [ ( ntrees + 1 ) ]
|
||||
+ this
|
||||
;
|
||||
set themin minsteps ;
|
||||
set themax maxsteps ;
|
||||
loop 0 ntrees
|
||||
progress #1 (ntrees+1) Calculating indices... ;
|
||||
set this length[#1] ;
|
||||
set CIs[#1] 'themin'/'this' ;
|
||||
set RIs[#1] ('themax'-'this')/('themax'-'themin') ;
|
||||
stop
|
||||
progress/ ;
|
||||
report= ;
|
||||
macfloat 3 ;
|
||||
maketable CIs Consistency index ;
|
||||
maketable RIs Retention index ;
|
||||
proc/ ;
|
||||
Loading…
Reference in New Issue