macro=; 
lquote [ ; 

if ( ntax < 3 ) 
 if ( windows ) 
      errmsg You must read the data set before running a quickie! ; 
 else errmsg &10&10You must read the data set (with &34proc filename.,&34) before running a quickie! ; end 
 end 

log aquickie.out; 

watch=; 

coll tbr ; 

drift : fitd 2 rfitd 0.1 ; 

var :
  i j
  plotapo bootit
  runquickie dobremer
  medium big verybig 
;


set medium 200 ;
set big 500 ; 
set verybig 1500 ;
set plotapo 0 ;
set runquickie 0 ; 
set dobremer 0 ;
set bootit 0 ; 

if ( ntax > 'medium' ) 
if ( !windows ) cls ; end 
if ( ntax < 'verybig' ) 
quote 
****************************************************
 This is a large data set.  A consensus estimation 
 instead of a complete search is recommended. 
****************************************************
; 
else 
quote 
*************************************************************
 This is a very large data set.  A consensus estimation 
 instead of a complete search is VERY STRONGLY RECOMMENDED 
*************************************************************
;
end 
if ( !windows ) quote &10&10(press key to continue); pause ; end 
set runquickie getresponse [ Run consensus estimation instead of a complete search? ] ;
if ( 'runquickie' == 2 ) proc/; end 
end

if ( !'runquickie' )
 if ( windows ) 
  quote * 
  TNT will find most parsimonious trees for the data set,
  with 20 independent hits to the best score, and then 
  calculate the strict consensus, calculate supports when
  requested, and save the results in file &34aquickie.out&34.
  The consensus tree will be saved to &34aquickie.nex&34  in
  Nexus format.;
  else 
  if ( !windows ) cls ; end 
  quote 
   &10
    TNT will find most parsimonious trees for the data set,
    with 20 independent hits to the best score, and then 
    calculate the strict consensus, calculate supports when
    requested, and save the results in file &34aquickie.out&34.
    The consensus tree will be saved to &34aquickie.nex&34  in
    Nexus format.&10&10
   (press any key to continue);
 pause ; 
 end 
 set plotapo getresponse [ Do you also wish to plot synapomorphies on the tree? ] ; 
else 
if ( windows ) 
 quote * 
 TNT will estimate the strict consensus tree for the data set,
 calculate approximate supports (when requested), and save the
 results in file &34aquickie.out&34.  The consensus tree will be
 saved to &34aquickie.nex&34  in Nexus format.;
 else 
 if ( !windows ) cls ; end 
 quote 
   &10
    TNT will estimate the strict consensus tree for the data set,
    calculate approximate supports (when requested), and save the
    results in file &34aquickie.out&34.  The consensus tree will be
    saved to &34aquickie.tre&34  in Nexus format.&10&10
   (press any key to continue);
 pause ; 
 end 
end 


set dobremer getresponse [ Approximmate bremer supports with TBR? ] ;
if ( 'dobremer' == 2 ) proc/; end 
set bootit getresponse [ Calculate group supports with resampling? ] ;
if ( 'bootit' == 2 ) proc/; end 


if ( !windows ) cls ; end
resettime ;
if ( 'dobremer' ) tsave * tmp.tre; end
if ( ( ntax > 'medium' ) && 'runquickie' ) 
  set 0 ntax / 70 ; 
  set 1 'i' / 2 ; 
  if ( 'i' < 2 ) set i 2 ; end 
  if ( 'j' < 3 ) set j 3 ; end 
  if ( 'j' > 20 ) set j 20 ; end 
  if ( 'i' > 30 ) set i 30 ; end  
  sec: xss'/.0i'-'/.0j'+3-1 gocomb 60 fuse 4 drift 5 combstart 5 ;
  if ( ntax < 'big' )
       quote &10 
        ------------------------------------------------------------
        Search routine used: 
           a quick consensus estimation (Goloboff &38 Farris 2001),
           with 15 replications (each with default &34xmult&34  but
           with 3 starting points instead of the default 5, and using 
           XSS --see Goloboff &38 Pol 2007).  The sectorial searches
           analyzing sectors of 60 or more taxa with a combined 
           strategy (5 starting points, 5 cycles of tree-drifting for
           each, fusing the results in 4 cycles).  Sectors selections:
           XSS dividing tree in '/.0i' to '/.0j' parts, 3 times., CSS
           and RSS with defaults.  For more details of CSS, RSS, 
           and tree-drifting, see Goloboff 1999., for details of
           XSS, see Goloboff &38 Pol 2007.  For details of &34xmult&34,
           see documentation of TNT.
           Note: for consensus calculation, trees TBR-collapsed. 
        ------------------------------------------------------------ ; 
       if ( 'dobremer' ) 
           qnelsen [ xmu = rep 3 xss ; save ; ] ;
       else
           qnelsen [ xmu = rep 3 xss ; ] ;
           end 

  else
   if ( ntax < 'verybig' ) 
       quote &10 
        ------------------------------------------------------------
        Search routine used: 
           a quick consensus estimation (Goloboff &38 Farris 2001),
           with 15 random addition sequences, plus TBR, and sectorial 
           searches using CSS (defaults), RSS (defaults), and 
           XSS (dividing tree in '/.0i' to '/.0j' parts, 3 times),
           analyzing sectors of 60 or more taxa with a combined 
           strategy (5 starting points, 5 cycles of tree-drifting for
           each, fusing the results in 4 cycles).  For details of 
           CSS, RSS, and tree-drifting, see Goloboff 1999., for details 
           of XSS, see Goloboff &38  Pol 2007.   For details of &34xmult&34,
           see documentation of TNT.
           Note: for consensus calculation, trees TBR-collapsed. 
        ------------------------------------------------------------ ; 
       if ( 'dobremer' ) 
          qnelsen [ mu1=ho1 ; sec=xss ; drift=iter5; save ; ] ;
       else
          qnelsen [ mu1=ho1 ; sec=xss ; drift=iter5; ] ;
          end 
   else 
       quote &10 
        ------------------------------------------------------------
        Search routine used: 
           a quick consensus estimation (Goloboff &38 Farris 2001),
           with 15 random addition sequences plus TBR.
           Note: for consensus calculation, trees TBR-collapsed. 
        ------------------------------------------------------------ ; 
       if ( 'dobremer' ) 
           qnelsen [ mu1=ho1 ; save ; ] ;
       else
           qnelsen [ mu1=ho1 ; ] ;
           end 

    end 
  end 
else 
  report +/1 ; 
       if ( !windows ) cls ; end 
       quote &10
        ------------------------------------------------------------
        Search routine used: 
           finding optimal score 20 times independently, using defaults
           of &34xmult&34  plus 10 cycles of tree-drifting (Goloboff
           1999).
           Note: for consensus calculation, trees TBR-collapsed. 
           ALSO NOTE: THIS IS AN OVERKILL FOR MOST DATA SETS!
        ------------------------------------------------------------ ; 
  hold 1000 ; 
  xmu = hit 20 drift 10 ;
  if ( 'dobremer' ) save ; end 
  nelsen * ; 
  if ( 'plotapo' ) 
       set i ntrees ; 
       if ( !windows ) cls ; end 
       quote &10
        ------------------------------------------------------------
        Synapomorphies of 'i' trees plotted on the strict 
        consensus.  Only unambiguous synapomorphies, occuring in 
        every tree, are indicated. This makes results much more 
        conservative! 
        ------------------------------------------------------------ ; 
       coll rule 3 ; 
       set i -- ; 
       if ( windows )
          log & aquickie_apo.emf ;
          end 
       apo [ 0.'i' ;
       if ( windows ) log /& ; end 
       coll tbr ; 
       end
  tchoose { strict } ; 
end     

if ( 'dobremer' )
   tsave / ; end
   quote &10
        ------------------------------------------------------------
        Group supports are calculated by TBR-swapping the trees
        found, keeping note of the number of steps needed to
        loose each group.  The labels on branches show absolute
        and relative bremer supports (Goloboff &38  Farris 2001).
        Groups indicated with a question mark (?) are those
        for which the absolute bremer supports appear to be
        10 or more... 
        ------------------------------------------------------------ ; 
   sub 10 ; 
   ttag= ;
   p tmp.tre ;
   bsupp !!+0 1. ;
   sub 10x0.90 ;
   bsupp [!!+0 1.; 
   if ( windows ) log & aquickie_brem.emf ; end 
   ttag;
   if ( windows ) log /& ; tplot [ ; end 
   sub 0 ;
   keep 1 ;
   ttag - ; 
   end


if ( 'bootit' ) 
  ttag = ;
  if ( !windows ) cls ; end 
  quote &10
        ------------------------------------------------------------
        Resampling is done with 100 replications of symmetric 
        resampling (see Goloboff et al. 2003), analyzing each data 
        set with a single random addition sequence plus TBR
        (collapsing the resulting tree with TBR, see Goloboff &38 
        Farris, 2001).  The labels on branches show frequency and 
        frequency differences (see Goloboff et al. 2003).
        ------------------------------------------------------------ ; 
  coll tbr ; 
  resample [ mu1=ho1; ] rep 100 freq gc from 0 ; 
  keep 1 ;   
  if ( windows ) log & aquickie.emf ; end 
  ttag ;
  if ( windows ) log /& ; tplot [ ; end 
  end


export - aquickie.tre ;
if ( windows )
  if ( 'bootit' ) 
     quote Tree-diagram (with bremer supports) saved to file aquickie_brem.emf  ;
     end
  if ( 'dobremer' )
     quote Tree-diagram (with supports) saved to file aquickie.emf  ;
     end 
  if ( 'plotapo' )
     quote Synapomorphies (as diagram) saved to file aquickie_apo.emf ;
     end
  end 
quote Results saved (as text) to file aquickie.out &10&10; 

log / ; 

set i time ; 
quote 
***************************************************
ANALYSIS COMPLETED (total time used: '/.0i' sec) 
***************************************************

               Please note!!

    ...for each of the quantities calculated 
    by this script, it is possible to use more
    exhaustive and accurate (but more time
    consuming) algorithms, or viceversa. The
    routines used by the script are only an
    approximation which provides a good tredoff
    between accuracy and run-times for most data
    sets


;

if ( !windows ) quote &10 

       You can now exit TNT, typing &34zzz&34 ;
end 

proc/;